Before running this script, you need to run all the analysis first so the variable are available.

run volcanos for all the comparisons of interest

Get comparisons

ls(all.names = TRUE)
 [1] ".Random.seed"                                               "adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"         "agbmi_df"                                                  
 [4] "base_path"                                                  "bone_hip_vs_tibia"                                          "bone_non_sclerotic_hip_vs_tibia"                           
 [7] "bone_sclerotic_hip_vs_tibia"                                "c"                                                          "col_sums"                                                  
[10] "color_palette"                                              "column_to_plot"                                             "common_genes"                                              
[13] "comparison_names"                                           "comparisons_list"                                           "df"                                                        
[16] "hip_adipocytes_sclerotic_vs_non_sclerotic"                  "hip_pellet_sclerotic_vs_non_sclerotic"                      "hip_sclerotic_vs_non_sclerotic"                            
[19] "m_pca_hip"                                                  "m_pca_hip_t"                                                "m_pca_hip_transposed_adipocytes"                           
[22] "m_pca_hip_transposed_pellet"                                "m_pca_samples_bone"                                         "m_pca_tibia"                                               
[25] "m_pca_tibia_t"                                              "m_pca_tibia_transposed_adipocytes"                          "m_pca_tibia_transposed_pellet"                             
[28] "m_samples_bone"                                             "matrix_counts_hip"                                          "matrix_counts_tibia"                                       
[31] "md"                                                         "md_df"                                                      "md_df_bone"                                                
[34] "md_df_hip"                                                  "md_df_split"                                                "md_df_tibia"                                               
[37] "mean_sum"                                                   "normalize_and_pca"                                          "p"                                                         
[40] "path"                                                       "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"           "percentiles"                                               
[43] "percentVar_obj"                                             "plot_the_pca"                                               "plot_volcano"                                              
[46] "pp"                                                         "quantiles"                                                  "results"                                                   
[49] "run_pca_structuring"                                        "run_pca_structuring_2"                                      "save_results_deg"                                          
[52] "sums_mm"                                                    "sums_mm_hip"                                                "sums_mm_tibia"                                             
[55] "test_diff_exp"                                              "tibia_adipocytes_sclerotic_vs_non_sclerotic"                "tibia_pellet_sclerotic_vs_non_sclerotic"                   
[58] "tibia_sclerotic_vs_non_sclerotic"                           "time_taken"                                                 "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"
[61] "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic" "volcano_hip_adipocytes_sclerotic_vs_non_sclerotic"          "volcano_hip_pellet_sclerotic_vs_non_sclerotic"             
[64] "volcano_hip_sclerotic_vs_non_sclerotic"                     "volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"   "volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic"       
[67] "volcano_tibia_pellet_sclerotic_vs_non_sclerotic"            "volcano_tibia_sclerotic_vs_non_sclerotic"                   "y"                                                         
[70] "y_norm"                                                     "y_normalized_corrected"                                     "y_normalized_corrected_pcas"                               
[73] "y_normalized_corrected_pcas_df"                            
# Get all object names that match a pattern
comparison_names <- ls(pattern = "vs")
comparison_names
 [1] "adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"         "bone_hip_vs_tibia"                                          "bone_non_sclerotic_hip_vs_tibia"                           
 [4] "bone_sclerotic_hip_vs_tibia"                                "hip_adipocytes_sclerotic_vs_non_sclerotic"                  "hip_pellet_sclerotic_vs_non_sclerotic"                     
 [7] "hip_sclerotic_vs_non_sclerotic"                             "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"           "tibia_adipocytes_sclerotic_vs_non_sclerotic"               
[10] "tibia_pellet_sclerotic_vs_non_sclerotic"                    "tibia_sclerotic_vs_non_sclerotic"                           "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"
[13] "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic" "volcano_hip_adipocytes_sclerotic_vs_non_sclerotic"          "volcano_hip_pellet_sclerotic_vs_non_sclerotic"             
[16] "volcano_hip_sclerotic_vs_non_sclerotic"                     "volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"   "volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic"       
[19] "volcano_tibia_pellet_sclerotic_vs_non_sclerotic"            "volcano_tibia_sclerotic_vs_non_sclerotic"                  
comparisons_list <- mget(comparison_names)
comparisons_list
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$results
Coefficient:  groupsclerotic 

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$colsums_samples

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$normalized_matrix
                          X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte
TSPAN6                                      6.204800e+00                       4.542855e+00                       1.862113e+01                   4.562555e+00                       9.878102e+00
TNMD                                        0.000000e+00                       0.000000e+00                       7.161971e+00                   1.520852e+00                       9.188932e-01
DPM1                                        9.996622e+00                       1.249285e+01                       4.297183e+00                   9.632061e+00                       1.608063e+01
SCYL3                                       8.962489e+00                       9.842853e+00                       1.002676e+01                   3.041703e+00                       2.297233e+00
C1orf112                                    0.000000e+00                       0.000000e+00                       0.000000e+00                   0.000000e+00                       2.297233e-01
FGR                                         3.998649e+01                       1.377999e+02                       2.291831e+01                   6.641052e+01                       3.928268e+01
CFH                                         1.378844e+00                       4.164284e+00                       1.432394e+00                   6.590357e+00                       4.135019e+00
FUCA2                                       2.688747e+01                       1.249285e+01                       4.297183e+00                   1.318071e+01                       1.171589e+01
GCLC                                        2.619804e+01                       2.763570e+01                       6.087676e+01                   9.125110e+00                       3.308015e+01
NFYA                                        1.792498e+01                       5.337855e+01                       3.437746e+01                   5.322981e+01                       2.021565e+01
STPG1                                       1.103076e+01                       3.785713e-01                       7.161971e-01                   5.576456e+00                       2.756680e+00
NIPAL3                                      8.962489e+00                       4.164284e+00                       1.647253e+01                   1.318071e+01                       3.216126e+00
LAS1L                                       3.136871e+01                       8.744996e+01                       3.509366e+01                   4.207690e+01                       4.663383e+01
ENPP4                                       0.000000e+00                       2.271428e+00                       7.161971e-01                   5.069506e-01                       6.202529e+00
SEMA3F                                      4.136533e+01                       8.744996e+01                       4.941760e+01                   3.345874e+01                       1.516174e+01
ANKIB1                                      1.378844e+01                       1.211428e+01                       1.289155e+01                   1.470157e+01                       1.378340e+01
CYP51A1                                     1.689084e+01                       6.814283e+00                       5.013380e+00                   1.165986e+01                       8.729485e+00
                          X109_tibia_sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte
TSPAN6                                      1.021426e+01                       7.349113e+00                   4.873022e+00                       7.805789e+00                       3.095194
TNMD                                        0.000000e+00                       0.000000e+00                   0.000000e+00                       0.000000e+00                       0.000000
DPM1                                        1.407299e+01                       1.561687e+01                   5.847626e+00                       1.059357e+01                      13.412508
SCYL3                                       2.950787e+00                       1.837278e+00                   4.873022e+00                       2.230225e+00                       0.000000
C1orf112                                    4.993640e+00                       0.000000e+00                   0.000000e+00                       5.575564e-01                       0.000000
FGR                                         8.284903e+01                       3.858284e+01                   3.411115e+01                       2.255316e+02                     206.346277
CFH                                         5.220624e+00                       1.837278e+00                   0.000000e+00                       1.115113e+00                       4.126926
FUCA2                                       1.770472e+01                       2.066938e+01                   1.656827e+01                       1.115113e+01                      12.380777
GCLC                                        3.563643e+01                       2.755917e+01                   3.800957e+01                       3.735628e+01                      26.825016
NFYA                                        1.838567e+01                       1.699482e+01                   5.652705e+01                       2.732026e+01                      17.539434
STPG1                                       6.355542e+00                       1.837278e+00                   2.923813e+00                       6.969455e+00                       0.000000
NIPAL3                                      8.171411e+00                       1.286095e+01                   8.771439e+00                       1.784180e+01                       4.126926
LAS1L                                       4.880148e+01                       3.628625e+01                   3.411115e+01                       2.927171e+01                      11.349045
ENPP4                                       1.815869e+00                       2.296598e+00                   3.898417e+00                       1.449647e+01                       4.126926
SEMA3F                                      2.564915e+01                       2.066938e+01                   2.144130e+01                       4.209551e+01                      15.475971
ANKIB1                                      9.987280e+00                       1.469823e+01                   3.313655e+01                       1.226624e+01                      16.507702
CYP51A1                                     1.725076e+01                       2.296598e+01                   1.266986e+01                       8.084567e+00                       3.095194
                          X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte
TSPAN6                                          4.669196e+00                   7.331045e+00                       5.444540e+00                   1.055755e+01                       1.277559e+01
TNMD                                            7.183378e-02                   0.000000e+00                       4.949581e-01                   0.000000e+00                       2.814961e+00
DPM1                                            1.249908e+01                   1.241548e+01                       1.666359e+01                   2.413154e+01                       1.429134e+01
SCYL3                                           3.591689e+00                   3.665522e+00                       2.969749e+00                   3.016443e+00                       2.598426e+00
C1orf112                                        1.149341e+00                   1.655397e+00                       3.134735e+00                   0.000000e+00                       0.000000e+00
FGR                                             2.295089e+02                   1.115028e+02                       2.479740e+02                   4.735816e+02                       5.283466e+01
CFH                                             1.795845e+00                   2.601338e+00                       3.299721e-01                   0.000000e+00                       5.629923e+00
FUCA2                                           1.537243e+01                   1.619924e+01                       1.600365e+01                   4.524665e+00                       1.710630e+01
GCLC                                            4.662013e+01                   3.027012e+01                       7.341879e+01                   1.266906e+02                       3.464568e+01
NFYA                                            3.103219e+01                   2.707757e+01                       4.306136e+01                   6.032886e+01                       3.139765e+01
STPG1                                           7.470714e+00                   1.891882e+00                       9.074233e+00                   9.049329e+00                       5.196852e+00
NIPAL3                                          1.530060e+01                   6.621589e+00                       1.484874e+01                   6.032886e+00                       8.877955e+00
LAS1L                                           3.598873e+01                   3.488158e+01                       3.695687e+01                   2.262332e+01                       3.486222e+01
ENPP4                                           2.729684e+00                   3.429037e+00                       4.619609e+00                   4.524665e+00                       1.234252e+01
SEMA3F                                          2.521366e+01                   1.454385e+01                       4.817593e+01                   1.809866e+01                       2.750001e+01
ANKIB1                                          1.206808e+01                   1.537155e+01                       1.666359e+01                   0.000000e+00                       1.364174e+01
CYP51A1                                         9.697561e+00                   1.135129e+01                       1.468376e+01                   1.508222e+00                       1.147638e+01
                          X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte
TSPAN6                                      1.149548e+01                       1.841704e+00                   0.000000e+00                       5.196115e+00                   7.432058e+00
TNMD                                        0.000000e+00                       0.000000e+00                   0.000000e+00                       0.000000e+00                   0.000000e+00
DPM1                                        9.405392e+00                       1.197108e+01                   2.775202e+01                       1.160063e+01                   1.300610e+01
SCYL3                                       7.315305e+00                       5.064687e+00                   0.000000e+00                       2.537638e+00                   4.645036e-01
C1orf112                                    6.966957e-01                       0.000000e+00                   0.000000e+00                       3.625197e-01                   0.000000e+00
FGR                                         5.329722e+01                       3.315068e+01                   1.591116e+02                       5.691559e+01                   5.388242e+01
CFH                                         4.528522e+00                       5.525113e+00                   9.250672e+00                       2.175118e+00                   6.038547e+00
FUCA2                                       1.602400e+01                       2.900685e+01                   1.480108e+01                       1.389659e+01                   2.647671e+01
GCLC                                        1.706904e+01                       2.900685e+01                   2.405175e+01                       3.673533e+01                   9.754576e+00
NFYA                                        3.692487e+01                       1.519406e+01                   0.000000e+00                       2.271790e+01                   2.926373e+01
STPG1                                       8.012000e+00                       1.243151e+01                   0.000000e+00                       5.800315e+00                   2.787022e+00
NIPAL3                                      1.254052e+01                       5.064687e+00                   1.850134e+01                       1.172147e+01                   7.432058e+00
LAS1L                                       2.717113e+01                       3.683409e+01                   1.850134e+01                       4.495244e+01                   4.691487e+01
ENPP4                                       4.876870e+00                       1.657534e+01                   0.000000e+00                       7.008713e+00                   6.503051e+00
SEMA3F                                      3.413809e+01                       1.887747e+01                   2.590188e+01                       1.595087e+01                   1.439961e+01
ANKIB1                                      1.428226e+01                       2.117960e+01                   1.480108e+01                       1.945522e+01                   7.896562e+00
CYP51A1                                     1.184383e+01                       1.841704e+00                   4.625336e+01                       8.217112e+00                   1.672213e+01
                          X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte X160_Tibia_non.sclerotic_adipocyte
TSPAN6                                          9.581084e+00                   2.545339e+00                       9.840294e+00                   8.902905e+00                       1.119467e+01
TNMD                                            1.532973e+00                   0.000000e+00                       1.192763e+00                   1.440176e+00                       9.950816e-01
DPM1                                            7.537119e+00                   9.454116e+00                       1.177853e+01                   1.112863e+01                       1.285314e+01
SCYL3                                           4.854416e+00                   1.818099e+00                       5.367433e+00                   3.927752e-01                       2.238934e+00
C1orf112                                        1.277478e+00                   0.000000e+00                       2.981907e-01                   2.618502e-01                       6.633877e-01
FGR                                             3.755785e+01                   2.654425e+01                       1.938240e+01                   2.867259e+01                       1.393114e+01
CFH                                             5.109912e-01                   1.090860e+00                       2.087335e+00                   2.094801e+00                       2.156010e+00
FUCA2                                           1.775694e+01                   7.636017e+00                       1.684778e+01                   1.911506e+01                       1.617008e+01
GCLC                                            3.232019e+01                   2.690787e+01                       3.339736e+01                   4.268158e+01                       3.681802e+01
NFYA                                            4.675569e+01                   2.581701e+01                       2.788083e+01                   3.155294e+01                       3.225723e+01
STPG1                                           9.581084e+00                   1.454479e+00                       3.727384e+00                   5.891628e+00                       8.126500e+00
NIPAL3                                          2.414433e+01                   8.726876e+00                       8.647531e+00                   1.086678e+01                       9.619122e+00
LAS1L                                           3.794109e+01                   5.127040e+01                       3.951027e+01                   4.150325e+01                       3.632048e+01
ENPP4                                           7.664867e+00                   3.636199e+00                       6.709292e+00                   4.058677e+00                       5.970489e+00
SEMA3F                                          3.359767e+01                   3.272579e+01                       2.683717e+01                   1.872229e+01                       2.073087e+01
ANKIB1                                          2.491082e+01                   1.563565e+01                       2.564440e+01                   1.754396e+01                       2.545750e+01
CYP51A1                                         8.686850e+00                   1.527203e+01                       1.118215e+01                   2.710149e+01                       1.459453e+01
                          X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6                                      8.639512e+00                       7.787759e+00                   6.838519e+00                       9.762750e+00                   2.026897e+00
TNMD                                        3.277056e+00                       9.461763e-01                   0.000000e+00                       0.000000e+00                   0.000000e+00
DPM1                                        1.241309e+01                       1.936022e+01                   8.703569e+00                       1.320843e+01                   3.378161e+00
SCYL3                                       3.277056e+00                       3.202443e+00                   2.362397e+00                       1.091131e+01                   4.053793e+00
C1orf112                                    7.944379e-01                       6.550452e-01                   1.119030e+00                       0.000000e+00                   0.000000e+00
FGR                                         2.065538e+01                       4.250515e+01                   4.457471e+01                       2.584257e+01                   1.361399e+02
CFH                                         3.773580e+00                       2.183484e+00                   1.616377e+00                       1.148559e+00                   1.351264e+00
FUCA2                                       1.529293e+01                       1.120855e+01                   1.131464e+01                       1.607982e+01                   3.411943e+01
GCLC                                        3.326709e+01                       2.612902e+01                   2.729191e+01                       2.239690e+01                   2.094460e+01
NFYA                                        3.426013e+01                       4.075837e+01                   2.934346e+01                       1.320843e+01                   1.520173e+01
STPG1                                       8.142988e+00                       4.730882e+00                   4.351785e+00                       7.465632e+00                   6.756322e+00
NIPAL3                                      1.022839e+01                       1.200916e+01                   1.317969e+01                       5.742794e+00                   1.553954e+01
LAS1L                                       4.160868e+01                       3.901158e+01                   2.654589e+01                       2.699113e+01                   4.459173e+01
ENPP4                                       2.979142e+00                       5.240361e+00                   4.227448e+00                       3.445676e+00                   2.702529e+00
SEMA3F                                      2.691158e+01                       3.384400e+01                   3.344657e+01                       1.148559e+01                   2.736311e+01
ANKIB1                                      1.588876e+01                       1.826848e+01                   1.603943e+01                       5.168515e+00                   1.655299e+01
CYP51A1                                     1.698111e+01                       1.448378e+01                   1.373921e+01                       3.445676e+00                   1.047230e+01
                          X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte
TSPAN6                                          2.361189e+01                      1.381167e+00                     5.865657e+00                 4.855878e+00                     5.007100e+00                 1.204236e+00
TNMD                                            0.000000e+00                      0.000000e+00                     9.776094e-01                 1.213970e+00                     0.000000e+00                 1.003530e-01
DPM1                                            1.453040e+01                      8.632296e+00                     1.309997e+01                 1.532637e+01                     1.301846e+01                 5.118002e+00
SCYL3                                           4.994823e+00                      0.000000e+00                     5.865657e+00                 3.034924e-01                     1.859780e+00                 2.007060e+00
C1orf112                                        4.540748e-01                      0.000000e+00                     1.173131e+00                 1.213970e+00                     3.576500e+00                 1.605648e+00
FGR                                             2.406597e+01                      1.022064e+02                     9.013559e+01                 7.966675e+01                     1.437753e+02                 5.814452e+02
CFH                                             4.540748e+00                      2.417043e+00                     5.865657e+00                 6.069848e+00                     1.430600e+00                 2.107413e+00
FUCA2                                           1.316817e+01                      1.173992e+01                     1.544623e+01                 8.042548e+00                     1.630884e+01                 2.017095e+01
GCLC                                            1.498447e+01                      3.211214e+01                     3.832229e+01                 4.097147e+01                     6.122968e+01                 5.890720e+01
NFYA                                            2.088744e+01                      3.556506e+01                     3.187007e+01                 4.294417e+01                     3.848314e+01                 5.118002e+01
STPG1                                           9.535572e+00                      6.905837e-01                     1.153579e+01                 1.062223e+01                     3.862620e+00                 4.917296e+00
NIPAL3                                          1.680077e+01                      1.622872e+01                     7.625354e+00                 2.063748e+01                     1.859780e+01                 1.334695e+01
LAS1L                                           3.178524e+01                      4.695969e+01                     6.178492e+01                 5.220069e+01                     6.366170e+01                 4.696520e+01
ENPP4                                           2.270374e+00                      7.941713e+00                     3.128350e+00                 2.579685e+00                     8.583599e-01                 1.605648e+00
SEMA3F                                          2.724449e+00                      2.106280e+01                     5.474613e+01                 4.688957e+01                     2.632304e+01                 1.605648e+01
ANKIB1                                          2.815264e+01                      1.726459e+01                     2.737306e+01                 2.215494e+01                     2.989954e+01                 2.308119e+01
CYP51A1                                         4.994823e+00                      1.622872e+01                     9.971616e+00                 1.502287e+01                     1.173092e+01                 1.123953e+01
                          X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte
TSPAN6                                        0.000000e+00                 7.092256e+00                     0.000000e+00                 2.811115e+00                     6.511858e+00                 2.097175e+00
TNMD                                          4.211673e-01                 3.546128e-01                     0.000000e+00                 3.513893e-01                     0.000000e+00                 2.621468e-01
DPM1                                          1.095035e+01                 6.737643e+00                     5.841804e+00                 7.379176e+00                     1.172134e+01                 2.123389e+01
SCYL3                                         4.632840e+00                 3.900741e+00                     2.596357e+00                 1.405557e+00                     5.860672e+00                 2.097175e+00
C1orf112                                      0.000000e+00                 0.000000e+00                     4.543625e+00                 1.054168e+00                     0.000000e+00                 2.359321e+00
FGR                                           9.560497e+01                 3.546128e+01                     4.290480e+02                 4.139366e+02                     2.031700e+02                 6.343953e+01
CFH                                           1.895253e+00                 0.000000e+00                     0.000000e+00                 0.000000e+00                     0.000000e+00                 1.572881e+00
FUCA2                                         2.211128e+01                 2.021293e+01                     9.087250e+00                 1.774516e+01                     2.409387e+01                 1.494237e+01
GCLC                                          2.295362e+01                 1.312067e+01                     5.257623e+01                 5.885771e+01                     4.753656e+01                 2.306892e+01
NFYA                                          4.043206e+01                 4.326276e+01                     2.823539e+01                 3.759866e+01                     2.539625e+01                 4.325423e+01
STPG1                                         2.316420e+00                 2.836902e+00                     4.543625e+00                 0.000000e+00                     9.116601e+00                 2.359321e+00
NIPAL3                                        1.263502e+01                 9.929158e+00                     1.914813e+01                 1.335279e+01                     1.758202e+01                 1.389378e+01
LAS1L                                         4.085322e+01                 4.964579e+01                     5.939167e+01                 5.516813e+01                     3.451285e+01                 3.067118e+01
ENPP4                                         5.896342e+00                 2.836902e+00                     0.000000e+00                 2.108336e+00                     1.497727e+01                 1.048587e+00
SEMA3F                                        1.137152e+01                 6.737643e+00                     9.736340e+00                 1.546113e+01                     1.823320e+01                 1.913672e+01
ANKIB1                                        2.337478e+01                 2.553212e+01                     2.174449e+01                 2.178614e+01                     2.018676e+01                 1.677740e+01
CYP51A1                                       6.949260e+00                 1.808525e+01                     6.815438e+00                 7.730565e+00                     0.000000e+00                 9.961580e+00
                          X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte
TSPAN6                                        3.356292e+00                 2.730114e+00                     3.850280e+00                 3.593039e+00                 8.596257e+00                     9.705544e-02
TNMD                                          4.475056e-01                 0.000000e+00                     4.052926e-01                 0.000000e+00                 0.000000e+00                     0.000000e+00
DPM1                                          1.253016e+01                 1.467437e+01                     1.205746e+01                 1.225860e+01                 1.124126e+01                     1.116138e+01
SCYL3                                         9.621371e+00                 3.412643e-01                     3.546310e+00                 3.522587e+00                 3.570753e+00                     2.523441e+00
C1orf112                                      4.475056e-01                 2.047586e+00                     4.154249e+00                 2.818070e+00                 7.935007e-01                     1.844053e+00
FGR                                           1.018075e+01                 1.979333e+01                     1.509715e+02                 2.305181e+02                 2.697902e+01                     3.838543e+02
CFH                                           1.454393e+00                 8.531608e+00                     1.215878e+00                 1.549938e+00                 2.248252e+00                     0.000000e+00
FUCA2                                         1.364892e+01                 2.081712e+01                     2.259506e+01                 1.261086e+01                 1.454751e+01                     1.543181e+01
GCLC                                          3.524107e+01                 1.603942e+01                     6.322565e+01                 8.130132e+01                 2.711127e+01                     9.200856e+01
NFYA                                          3.210853e+01                 4.095172e+01                     5.126952e+01                 5.805224e+01                 2.697902e+01                     6.755059e+01
STPG1                                         1.286579e+01                 1.228552e+01                     4.762188e+00                 3.663491e+00                 2.645002e+00                     3.979273e+00
NIPAL3                                        2.080901e+01                 9.214136e+00                     2.411491e+01                 2.064236e+01                 9.257508e+00                     3.561935e+01
LAS1L                                         5.381255e+01                 5.118965e+01                     4.306234e+01                 4.360963e+01                 3.504628e+01                     5.173055e+01
ENPP4                                         4.027551e+00                 6.825286e-01                     4.863512e+00                 4.297557e+00                 6.612506e+00                     4.076328e+00
SEMA3F                                        2.886411e+01                 2.320597e+01                     2.066992e+01                 2.184004e+01                 1.811827e+01                     6.890936e+00
ANKIB1                                        3.703109e+01                 3.378517e+01                     2.452020e+01                 2.867386e+01                 2.645002e+01                     1.087021e+01
CYP51A1                                       5.593820e+00                 9.555401e+00                     6.889975e+00                 8.313306e+00                 8.199507e+00                     3.591051e+00
                          X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte
TSPAN6                                    1.339373e+00                     2.620246e+00                 3.098215e+00                     3.459986e+00                 0.000000e+00                     4.200378e+00
TNMD                                      0.000000e+00                     1.588028e-01                 0.000000e+00                     0.000000e+00                 0.000000e+00                     6.269221e-02
DPM1                                      6.929801e+00                     9.845774e+00                 1.206673e+01                     7.284181e+00                 5.960893e+00                     1.003075e+01
SCYL3                                     5.182792e+00                     3.890669e+00                 4.402727e+00                     3.642091e+00                 4.967411e+00                     4.451147e+00
C1orf112                                  3.202849e+00                     1.905634e+00                 3.016683e+00                     1.638941e+00                 1.490223e+00                     4.200378e+00
FGR                                       3.780527e+02                     1.392701e+02                 1.022411e+02                     1.358500e+02                 1.316364e+02                     2.121504e+02
CFH                                       5.241026e-01                     1.429225e+00                 3.668939e+00                     7.284181e-01                 0.000000e+00                     4.200378e+00
FUCA2                                     1.956650e+01                     2.040616e+01                 1.386044e+01                     8.558913e+00                 1.043156e+01                     2.031228e+01
GCLC                                      1.259011e+02                     6.995264e+01                 4.900072e+01                     6.227975e+01                 6.954375e+01                     1.201810e+02
NFYA                                      5.858302e+01                     3.954190e+01                 3.986914e+01                     3.769564e+01                 5.215781e+01                     4.344570e+01
STPG1                                     4.891624e+00                     7.622535e+00                 4.647323e+00                     7.284181e-01                 4.967411e-01                     5.078069e+00
NIPAL3                                    3.377550e+01                     2.977553e+01                 1.932308e+01                     2.968304e+01                 3.228817e+01                     2.357227e+01
LAS1L                                     6.493049e+01                     4.597341e+01                 5.397417e+01                     5.535978e+01                 4.520344e+01                     5.090607e+01
ENPP4                                     6.114530e+00                     4.764084e+00                 4.891919e+00                     2.367359e+00                 0.000000e+00                     3.259995e+00
SEMA3F                                    4.775157e+00                     2.255000e+01                 2.584564e+01                     3.605670e+01                 1.142504e+01                     1.899574e+01
ANKIB1                                    2.300228e+01                     2.445563e+01                 2.225823e+01                     2.786199e+01                 1.589571e+01                     2.294535e+01
CYP51A1                                   5.823362e+00                     1.032218e+01                 9.213113e+00                     2.003150e+00                 1.986964e+00                     5.328838e+00
                          X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte X158_Hip_sclerotic_adipocyte
TSPAN6                                    1.632528e+00                     7.040817e+00                 1.150174e+01
TNMD                                      2.098965e+00                     0.000000e+00                 0.000000e+00
DPM1                                      1.306022e+01                     1.920223e+00                 1.461032e+01
SCYL3                                     7.229767e+00                     6.400743e+00                 8.704023e+00
C1orf112                                  6.996549e-01                     0.000000e+00                 2.331435e+00
FGR                                       1.604542e+02                     3.456401e+01                 3.559324e+01
CFH                                       0.000000e+00                     0.000000e+00                 2.642293e+00
FUCA2                                     1.306022e+01                     6.400743e-01                 1.507661e+01
GCLC                                      5.457308e+01                     6.144713e+01                 3.947896e+01
NFYA                                      4.711010e+01                     5.120594e+00                 4.010068e+01
STPG1                                     3.964711e+00                     0.000000e+00                 1.305603e+01
NIPAL3                                    1.166091e+01                     1.024119e+01                 1.025831e+01
LAS1L                                     4.081320e+01                     5.120594e+01                 4.600698e+01
ENPP4                                     8.395859e+00                     0.000000e+00                 3.108579e-01
SEMA3F                                    2.448792e+01                     5.888683e+01                 3.543781e+01
ANKIB1                                    2.565401e+01                     1.408163e+01                 3.978982e+01
CYP51A1                                   5.364021e+00                     1.152134e+01                 2.253720e+01
 [ reached getOption("max.print") -- omitted 22996 rows ]

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) patientX104 patientX105 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149   patientX150
TSPAN6     -11.81261 -0.48479544   0.4799604  -0.2372331   0.3982336  -0.8313460 -0.61786914 -0.10378028  -1.4153849  -0.1958023  -0.5294125  -0.1017646  -0.7996911  -0.5949694   0.1148174   0.5806153  3.250771e-01
TNMD       -16.88876 -0.80307457   4.7493835   3.6948424   2.4478087   1.0673836  2.57413713 -0.59587521   2.1922774  -0.6626219   1.9760162   0.4995742   1.9331888   1.6649122   2.2137261   3.5097190 -2.549059e-15
DPM1       -11.50302  0.21432770  -0.3454353   0.3480624   0.4058605  -0.1072695 -0.11985162  0.10072213  -0.4111277   0.1650724   0.5092445   0.2155536   0.3007711   0.1913979   0.6848698   0.1692601  1.171145e-01
SCYL3      -11.20402 -0.32264134  -0.6152666  -1.4438349  -1.3935654  -1.7050781 -0.95047190 -1.18119375  -1.7421457  -2.1680747  -1.1105934  -1.0900598  -0.9254745  -1.1144629  -1.3550943  -0.7102205 -9.167936e-01
C1orf112   -17.77735  0.08551583   0.0348957   4.1129396   4.8517373   4.8924915  0.05207893  0.05687388   4.9668596   3.0131425   4.1636040   4.2636889   4.0891881   5.1817388   4.6093492   2.8014721  3.670812e+00
         patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164  patientX99 groupsclerotic
TSPAN6   -1.68209474  -2.1154283 -0.84820389  -1.2799761 -0.07027376  -0.1289854  -0.8446642   0.3545509   0.3235262   0.3733027   0.0748689 -0.21224373   1.1597247 -1.66507892   -0.174245174
TNMD     -0.67750790  -0.3584921  0.96831960  -0.6152991 -0.64836657   2.9788467   3.9069215  -0.2293990   3.8716593   4.4995441   2.4184572 -0.37110727  -0.8030746 -0.80307457   -0.803074569
DPM1      0.62995734  -0.1068463  0.08775776  -0.4070299  0.19993602  -0.1724064   0.1359955  -0.1170109   0.1315259   0.2295348   0.3322944 -0.22349279   0.3651815 -0.15457785   -0.008168107
SCYL3    -1.37708650  -0.9588707 -0.94422319  -0.9177319 -1.99936756  -1.2437641  -0.5813295  -0.3139428  -1.4989824  -1.3289580  -1.3827485 -0.46676433  -0.9989474 -6.48781839   -0.416132542
C1orf112  0.06737776   4.8440978  4.81957552   4.3886832  2.57888114   3.6348894   4.8726564   4.1750433   2.7178726   3.6278944   3.8138792  0.03144956   3.2169856  0.08551583    0.085515829
23008 more rows ...

$fitted.values
         X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6                     1.800000e+01                       1.200000e+01                       1.668800e+01                   1.981073e+01                          47.934152                     40.7647533
TNMD                       3.069639e-09                       2.791350e-09                       8.083928e+00                   4.003878e+00                           2.275506                      0.8073838
DPM1                       2.900000e+01                       3.300000e+01                       9.954496e+00                   1.394775e+01                          65.883642                     66.1311608
SCYL3                      2.600000e+01                       2.600000e+01                       1.025451e+01                   9.520703e+00                          14.634147                      9.7334062
C1orf112                   1.840681e-08                       1.672647e-08                       8.416104e-09                   1.301153e-08                          10.467413                     11.5931102
         X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6                         1.449343e+01                   5.739670e+00                       2.177644e+01                   4.944339e+00                         92.8496869                     47.3984671
TNMD                           3.198689e-09                   5.285061e-10                       4.999326e-09                   4.735819e-10                          0.7138543                      0.1520392
DPM1                           2.427451e+01                   1.134632e+01                       4.265606e+01                   1.143118e+01                        174.1327125                    104.9187216
SCYL3                          9.063175e+00                   2.807074e+00                       5.515607e+00                   9.794278e-01                         63.5167672                     25.3588708
C1orf112                       1.330753e-08                   6.863320e-09                       1.321964e+00                   3.908965e-01                         18.5006337                     12.2996087
         X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6                            50.229711                     4.61712943                          61.049536                     31.8880249                       2.949810e+00                   6.168506e-01
TNMD                               2.505426                     0.09608491                           7.164189                      1.5612572                       2.921631e-09                   2.549021e-10
DPM1                             121.295707                    13.15968722                          55.149366                     33.9996581                       4.113865e+01                   1.015371e+01
SCYL3                             21.167203                     1.52171219                          30.882363                     12.6157610                       7.421578e+00                   1.213780e+00
C1orf112                          11.466970                     1.37271657                           1.345312                      0.9151433                       1.340134e-08                   3.649683e-09
         X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6                         5.696590e+01                   1.245276e+01                          50.813769                     15.0008714                          68.529011                      65.576020
TNMD                           1.197566e-08                   1.092225e-09                           7.111116                      0.8758606                          17.581948                       7.019396
DPM1                           1.019067e+02                   2.629311e+01                          66.377244                     23.1282657                          77.123823                      87.105968
SCYL3                          1.508364e+01                   2.578780e+00                          30.577258                      7.0597821                          20.239592                      15.147119
C1orf112                       1.923427e+00                   5.475794e-01                           5.495974                      2.1130052                           1.795816                       2.237965
         X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6                           129.518018                      90.879716                         109.407627                     107.630721                       1.039545e+01                   1.484962e+01
TNMD                              61.889209                      18.118151                           6.797086                       2.789803                       3.084098e-09                   1.838072e-09
DPM1                             152.972552                     126.689042                         193.176061                     224.300750                       1.402735e+01                   2.365029e+01
SCYL3                             43.275243                      23.748378                          46.678623                      35.914048                       1.484502e+01                   1.658481e+01
C1orf112                           8.375582                       7.653721                          11.544490                      14.790547                       1.048149e-08                   1.949916e-08
         X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte
TSPAN6                         5.200000e+01                      4.000000e+00                        29.777197                    32.239676                       22.3961831                   26.8281783
TNMD                           2.327208e-09                      3.060380e-09                        11.198430                     5.058551                        0.8461317                    0.4228802
DPM1                           3.200000e+01                      2.500000e+01                        73.055525                    93.357385                       63.2709574                   89.4561808
SCYL3                          1.100000e+01                      1.728099e-07                        16.314537                    13.814630                       17.1594974                   16.0760523
C1orf112                       1.000000e+00                      1.833858e-08                         5.833664                     8.225629                       17.5646048                   27.4016298
         X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte
TSPAN6                       1.885374e+01                 9.407993e+00                         5.476127                    8.4999953                        6.6655817                   13.9132196
TNMD                         3.115819e+00                 6.486851e-01                         1.445280                    0.9359646                        0.5549299                    0.4832701
DPM1                         4.244578e+01                 2.499901e+01                        20.565932                   37.6775215                       25.7779132                   63.5076604
SCYL3                        2.492546e+01                 9.727480e+00                         7.281516                    8.8394382                        6.8575440                   11.1947877
C1orf112                     2.886827e-08                 1.876036e-08                         8.348386                   16.8759607                        1.8431623                    5.0104186
         X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte
TSPAN6                          29.568123                    8.1451796                         40.11215                    48.475480                 6.500000e+01                     8.975745e+00
TNMD                             2.734187                    0.3142442                          2.16517                     1.091693                 7.990104e-09                     1.800023e-08
DPM1                           121.769418                   39.5916778                        120.50151                   171.880838                 8.500000e+01                     9.330226e+01
SCYL3                           48.046261                   10.3512827                         43.93949                    41.529712                 2.700000e+01                     5.367082e+01
C1orf112                         9.932282                    3.5632541                         33.17083                    52.206362                 6.000000e+00                     2.462140e+01
         X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte
TSPAN6                   1.257031e+01                        39.670966                   32.4640180                     1.120266e+01                 3.450969e+00                         50.43833
TNMD                     1.051758e-08                         1.215709                    0.4150699                     8.095297e-09                 1.040435e-09                         45.99004
DPM1                     1.542255e+02                       138.606364                  133.8756016                     3.680322e+01                 1.338119e+01                        184.23950
SCYL3                    5.878564e+01                        66.544738                   42.5893378                     2.979532e+01                 7.178367e+00                        121.36210
C1orf112                 4.490647e+01                        29.363663                   31.2939628                     8.289657e+00                 3.325656e+00                         39.32311
         X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte X158_Hip_sclerotic_adipocyte
TSPAN6                      11.393075                     1.646668e+01                 5.698149e+01
TNMD                         4.334172                     3.112427e-09                 4.493544e-09
DPM1                        49.119253                     1.400652e+01                 5.720666e+01
SCYL3                       21.439813                     1.554281e+01                 4.206440e+01
C1orf112                    11.567751                     1.897504e+00                 8.551283e+00
23008 more rows ...

$deviance
[1] 42.89574 17.54976 18.31456 25.97746 18.86381
23008 more elements ...

$iter
[1]  9 20  6 18 19
23008 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
23008 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6                               18                                 12                                 26                              9                                 43                             45
TNMD                                  0                                  0                                 10                              3                                  4                              0
DPM1                                 29                                 33                                  6                             19                                 70                             62
SCYL3                                26                                 26                                 14                              6                                 10                             13
C1orf112                              0                                  0                                  0                              0                                  1                             22
         X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6                                   16                              5                                 28                              3                                 65                             62
TNMD                                      0                              0                                  0                              0                                  1                              0
DPM1                                     34                              6                                 38                             13                                174                            105
SCYL3                                     4                              5                                  8                              0                                 50                             31
C1orf112                                  0                              0                                  2                              0                                 16                             14
         X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6                                   33                              7                                 59                             33                                  4                              0
TNMD                                      3                              0                                 13                              0                                  0                              0
DPM1                                    101                             16                                 66                             27                                 26                             15
SCYL3                                    18                              2                                 12                             21                                 11                              0
C1orf112                                 19                              0                                  0                              2                                  0                              0
         X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6                                   43                             16                                 75                              7                                 66                             68
TNMD                                      0                              0                                 12                              0                                  8                             11
DPM1                                     96                             28                                 59                             26                                 79                             85
SCYL3                                    21                              1                                 38                              5                                 36                              3
C1orf112                                  3                              0                                 10                              0                                  2                              2
         X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6                                  135                             87                                107                            110                                 17                              6
TNMD                                     12                             33                                 13                              0                                  0                              0
DPM1                                    155                            125                                266                            140                                 23                             10
SCYL3                                    27                             33                                 44                             38                                 19                             12
C1orf112                                  8                              8                                  9                             18                                  0                              0
         X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte
TSPAN6                                   52                                 4                               30                           32                               35                           12
TNMD                                      0                                 0                                5                            8                                0                            1
DPM1                                     32                                25                               67                          101                               91                           51
SCYL3                                    11                                 0                               30                            2                               13                           20
C1orf112                                  1                                 0                                6                            8                               25                           16
         X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte
TSPAN6                                  0                           20                                0                           16                               10                            8
TNMD                                    2                            1                                0                            2                                0                            1
DPM1                                   52                           19                               18                           42                               18                           81
SCYL3                                  22                           11                                8                            8                                9                            8
C1orf112                                0                            0                               14                            6                                0                            9
         X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte
TSPAN6                                 30                            8                               38                           51                           65                                1
TNMD                                    4                            0                                4                            0                            0                                0
DPM1                                  112                           43                              119                          174                           85                              115
SCYL3                                  86                            1                               35                           50                           27                               26
C1orf112                                4                            6                               41                           40                            6                               19
         X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte
TSPAN6                             23                               33                           38                               19                            0                               67
TNMD                                0                                2                            0                                0                            0                                1
DPM1                              119                              124                          148                               40                           12                              160
SCYL3                              89                               49                           54                               20                           10                               71
C1orf112                           55                               24                           37                                9                            3                               67
         X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte X158_Hip_sclerotic_adipocyte
TSPAN6                              7                               11                           74
TNMD                                9                                0                            0
DPM1                               56                                3                           94
SCYL3                              31                               10                           56
C1orf112                            3                                0                           15
23008 more rows ...

$unshrunk.coefficients
         (Intercept) patientX104 patientX105 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149  patientX150
TSPAN6     -11.81618  -0.4857755   0.4815589  -0.2376713   0.3996172  -0.8349319 -0.62049230 -0.10364519  -1.4242652  -0.1958416  -0.5313343  -0.1017497  -0.8029949  -0.5970923   0.1153811   0.5823536  0.326003704
TNMD       -33.43411  -1.0494932  21.3746761  20.4022888  18.9699210  17.5070267 19.19721780 -0.71993593  18.8615692  -0.7727034  18.6007244  16.6481213  18.4340716  18.1016566  18.7351626  20.0576922 -0.001367914
DPM1       -11.50502   0.2146616  -0.3462706   0.3486418   0.4065154  -0.1075598 -0.12013989  0.10092276  -0.4121912   0.1653354   0.5100628   0.2159223   0.3012737   0.1917270   0.6858420   0.1695494  0.117343619
SCYL3      -11.20267  -0.3260937  -0.6189212  -1.4528657  -1.4003615  -1.7147787 -0.95482187 -1.18662893  -1.7528323  -2.1825964  -1.1164502  -1.0949358  -0.9310356  -1.1194661  -1.3622807  -0.7126548 -0.920271480
C1orf112   -32.78125   0.0881163   0.0388218  19.0973027  19.8431275  19.8871350  0.04734518  0.05279574  19.9624765  17.9675199  19.1482629  19.2501450  19.0711701  20.1779711  19.6033168  17.7323656 18.644293046
         patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164   patientX99 groupsclerotic
TSPAN6   -1.69319335  -2.1372783 -0.85195087  -1.2863545 -0.07016719  -0.1288612  -0.8480978   0.3558369   0.3247568   0.3746516   0.0754737 -0.21260239   1.1624193  -1.67640213   -0.174008023
TNMD     -0.80812864  -0.5467559 17.28068609  -0.7165589 -0.73508057  19.5225599  20.6775048  -0.4154361  20.5823017  21.2541067  18.9148164 -0.53304780  -1.0494915  -1.04949397   -1.048156435
DPM1      0.63085027  -0.1071237  0.08790375  -0.4080840  0.20027378  -0.1728381   0.1362234  -0.1171433   0.1317481   0.2299263   0.3328313 -0.22412561   0.3657476  -0.15498446   -0.008247751
SCYL3    -1.38405040  -0.9624428 -0.94820405  -0.9216624 -2.01251730  -1.2502801  -0.5835787  -0.3154125  -1.5083677  -1.3350958  -1.3898287 -0.46981412  -1.0044373 -19.24727852   -0.419791314
C1orf112  0.06222665  19.8368834 19.81225914  19.3775746 17.50656019  18.6120588  19.8680347  19.1601089  17.6480311  18.6012238  18.7916730  0.03744615  18.1762472   0.08811633    0.090146465
23008 more rows ...

$df.residual
[1] 25 25 25 25 25
23008 more elements ...

$design
                                   (Intercept) patientX104 patientX105 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148
X102_tibia_sclerotic_adipocyte               1           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X104_tibia_non.sclerotic_adipocyte           1           1           0           0           0           0           0           0           0           0           0           0           0           0           0
X105_tibia_non.sclerotic_adipocyte           1           0           1           0           0           0           0           0           0           0           0           0           0           0           0
X105_tibia_sclerotic_adipocyte               1           0           1           0           0           0           0           0           0           0           0           0           0           0           0
X109_tibia_non.sclerotic_adipocyte           1           0           0           0           1           0           0           0           0           0           0           0           0           0           0
                                   patientX149 patientX150 patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164
X102_tibia_sclerotic_adipocyte               0           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X104_tibia_non.sclerotic_adipocyte           0           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X105_tibia_non.sclerotic_adipocyte           0           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X105_tibia_sclerotic_adipocyte               0           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X109_tibia_non.sclerotic_adipocyte           0           0           0           0           0           0           0           0           0           0           0           0           0           0           0
                                   patientX99 groupsclerotic
X102_tibia_sclerotic_adipocyte              0              1
X104_tibia_non.sclerotic_adipocyte          0              0
X105_tibia_non.sclerotic_adipocyte          0              0
X105_tibia_sclerotic_adipocyte              0              1
X109_tibia_non.sclerotic_adipocyte          0              0
52 more rows ...

$offset
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]   [,13]    [,14]    [,15]    [,16]    [,17]    [,18]   [,19]   [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 14.88056 14.78686 14.14931 14.49485 15.28639 15.29839 14.59352 13.84123 15.09285 13.78427 16.44891 15.95053 15.6174 13.40458 15.34551 14.87006 14.59111 13.20025 15.9288 14.5823 15.87321 14.82716 15.71868 15.84864
        [,25]    [,26]    [,27]    [,28]    [,29]    [,30]  [,31]    [,32]    [,33]    [,34] [,35]    [,36]    [,37]    [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]
[1,] 16.30535 16.12507 16.43579 16.59342 14.37015 14.90076 14.605 14.87888 15.44759 15.70106 15.76 16.11457 15.37338 14.85224 14.94084 15.55452 14.24447 15.15436 16.00587 14.89061 16.10495 16.46834 15.83857 16.14798
       [,49]    [,50]    [,51]    [,52]   [,53]    [,54]    [,55]    [,56]    [,57]
[1,] 16.6588 16.34875 16.32227 15.51868 14.5152 16.58503 15.27129 14.26168 15.67708
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 57
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23008 more rows ...

$dispersion
[1] 0.3697942 2.0625567 0.2254943 0.5069176 1.1407601
23008 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  2.6401182 -0.2538736  3.5734554  2.0828518  0.7060840
23008 more elements ...

$df.residual.zeros
[1] 25 17 25 25 20
23008 more elements ...

$df.prior
[1] 33.27426 33.27426 33.27426 33.27426 33.27426
23008 more elements ...

$var.post
[1] 1.467260 1.216406 0.958906 1.210280 1.203960
23008 more elements ...

$var.prior
[1] 1.280502 1.310447 1.128950 1.338895 1.360699
23008 more elements ...

$samples
52 more rows ...

$genes
23008 more rows ...


$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.707195

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.8389657

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.578436

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.353039


$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.933007 2.933007

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 1.0733833 0.7937281



$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$boxplot_gg


$bone_hip_vs_tibia
$bone_hip_vs_tibia$name
[1] "tibia-vs-hip"

$bone_hip_vs_tibia$results
Coefficient:  grouptibia 

$bone_hip_vs_tibia$colsums_samples

$bone_hip_vs_tibia$normalized_matrix
                          X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6                                       2.482204e-01                   6.436249e+00                9.248072e+00                       4.467957e+00                    5.313580e+00                       1.911082e+01
TNMD                                         0.000000e+00                   0.000000e+00                0.000000e+00                       0.000000e+00                    3.125635e-01                       7.350317e+00
DPM1                                         1.464500e+01                   1.036951e+01                1.387211e+01                       1.228688e+01                    1.781612e+01                       4.410190e+00
SCYL3                                        5.047148e+00                   9.296804e+00                3.302883e+00                       9.680573e+00                    2.187945e+00                       1.029044e+01
C1orf112                                     5.874549e+00                   0.000000e+00                0.000000e+00                       0.000000e+00                    2.813072e+00                       0.000000e+00
FGR                                          1.105574e+03                   4.147805e+01                2.057696e+02                       1.355280e+02                    1.184616e+02                       2.352101e+01
CFH                                          7.446611e-01                   1.430278e+00                3.633171e+00                       4.095627e+00                    1.562818e+00                       1.470063e+00
FUCA2                                        1.141814e+01                   2.789041e+01                1.915672e+01                       1.228688e+01                    5.938707e+00                       4.410190e+00
                          X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6                                      4.724198e+00                       1.058919e+01                   1.066013e+01                7.157967e+00                       7.291801e+00                    7.286609e+00
TNMD                                        1.574733e+00                       9.850405e-01                   0.000000e+00                0.000000e+00                       0.000000e+00                    0.000000e+00
DPM1                                        9.973307e+00                       1.723821e+01                   1.468730e+01                7.157967e+00                       1.549508e+01                    1.486468e+01
SCYL3                                       3.149465e+00                       2.462601e+00                   3.079594e+00                6.507243e+00                       1.822950e+00                    2.331715e+00
C1orf112                                    0.000000e+00                       2.462601e-01                   5.211621e+00                0.000000e+00                       0.000000e+00                    5.829287e-01
FGR                                         6.876333e+01                       4.211048e+01                   8.646554e+01                7.288112e+01                       3.828196e+01                    1.614713e+02
CFH                                         6.823842e+00                       4.432682e+00                   5.448513e+00                2.602897e+00                       1.822950e+00                    6.800835e-01
FUCA2                                       1.364768e+01                       1.255927e+01                   1.847757e+01                1.800337e+01                       2.050819e+01                    1.097849e+01
                          X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6                                      4.734692e+00                3.518309e+00                       7.830008e+00                    4.854921e-01                       3.040348                1.416696e+01
TNMD                                        0.000000e+00                0.000000e+00                       0.000000e+00                    0.000000e+00                       0.000000                0.000000e+00
DPM1                                        5.681631e+00                1.348685e+01                       1.062644e+01                    1.929831e+01                      13.174842                2.990802e+01
SCYL3                                       4.734692e+00                3.518309e+00                       2.237145e+00                    1.941968e+00                       0.000000                1.101875e+01
C1orf112                                    0.000000e+00                0.000000e+00                       5.592863e-01                    2.791580e+00                       0.000000                0.000000e+00
FGR                                         3.314285e+01                8.385302e+01                       2.262313e+02                    4.038081e+02                     202.689872                8.972407e+01
CFH                                         0.000000e+00                4.104693e+00                       1.118573e+00                    7.282382e-01                       4.053797                6.296426e+00
FUCA2                                       1.609795e+01                2.052347e+01                       1.118573e+01                    1.189456e+01                      12.161392                3.148213e+00
                          X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6                                          4.639200e+00                    2.580648e+00                   7.499628e+00                6.431380e+00                       5.360471e+00                    7.804782e-01
TNMD                                            7.137230e-02                    0.000000e+00                   0.000000e+00                2.046348e+00                       4.873156e-01                    0.000000e+00
DPM1                                            1.241878e+01                    2.163774e+01                   1.270098e+01                1.315510e+01                       1.640629e+01                    1.634413e+01
SCYL3                                           3.568615e+00                    3.771716e+00                   3.749814e+00                5.554374e+00                       2.923893e+00                    1.698688e+00
C1orf112                                        1.141957e+00                    3.672461e+00                   1.693464e+00                1.169342e+00                       3.086332e+00                    3.443286e+00
FGR                                             2.280345e+02                    3.479905e+02                   1.140669e+02                4.882002e+01                       2.441451e+02                    6.137313e+02
CFH                                             1.784308e+00                    3.970228e-01                   2.661158e+00                4.677367e+00                       3.248770e-01                    2.754629e-01
FUCA2                                           1.527367e+01                    1.826305e+01                   1.657176e+01                4.969703e+00                       1.575654e+01                    9.182096e+00
                          X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6                                      9.860365e+00                       1.324182e+01                    8.053954e+00                      11.979693                    9.741978                       1.860788e+00
TNMD                                        0.000000e+00                       2.917689e+00                    0.000000e+00                       0.000000                    0.000000                       0.000000e+00
DPM1                                        2.253798e+01                       1.481288e+01                    1.073861e+01                       9.801567                    0.000000                       1.209512e+01
SCYL3                                       2.817247e+00                       2.693252e+00                    2.147721e+00                       7.623441                    1.391711                       5.117167e+00
C1orf112                                    0.000000e+00                       0.000000e+00                    0.000000e+00                       0.726042                    0.000000                       0.000000e+00
FGR                                         4.423078e+02                       5.476279e+01                    1.310110e+02                      55.542213                   89.069514                       3.349419e+01
CFH                                         0.000000e+00                       5.835379e+00                    7.517024e+00                       4.719273                   27.834223                       5.582364e+00
FUCA2                                       4.225871e+00                       1.773057e+01                    6.443163e+00                      16.698966                   11.133689                       2.930741e+01
                          X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6                                       1.245728e+01                        0.00000                4.880715e+01                       5.603605e+00                    8.240529e+00                   7.565327e+00
TNMD                                         0.000000e+00                        0.00000                0.000000e+00                       0.000000e+00                    0.000000e+00                   0.000000e+00
DPM1                                         1.423689e+01                       27.28395                4.880715e+00                       1.251037e+01                    1.278703e+01                   1.323932e+01
SCYL3                                        6.821844e+00                        0.00000                6.507621e+00                       2.736644e+00                    0.000000e+00                   4.728329e-01
C1orf112                                     1.186408e+00                        0.00000                0.000000e+00                       3.909492e-01                    8.524686e-01                   0.000000e+00
FGR                                          5.398155e+01                      156.42798                3.253810e+01                       6.137902e+01                    1.344059e+02                   5.484862e+01
CFH                                          2.966019e+00                        9.09465                1.626905e+01                       2.345695e+00                    1.136625e+00                   6.146828e+00
FUCA2                                        1.571990e+01                       14.55144                0.000000e+00                       1.498639e+01                    7.103905e+00                   2.695148e+01
                          X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6                                   3.858497e+00                       1.001714e+01                    2.983326e+01                   2.639900e+00                1.480583e+01                       1.058055e+01
TNMD                                     0.000000e+00                       1.602742e+00                    0.000000e+00                   0.000000e+00                0.000000e+00                       1.282491e+00
DPM1                                     1.234719e+01                       7.880147e+00                    1.376920e+01                   9.805344e+00                2.035802e+01                       1.266460e+01
SCYL3                                    7.716993e-01                       5.075349e+00                    4.589733e+00                   1.885643e+00                9.253645e-01                       5.771208e+00
C1orf112                                 0.000000e+00                       1.335618e+00                    1.147433e+00                   0.000000e+00                9.253645e-01                       3.206227e-01
FGR                                      8.874542e+01                       3.926717e+01                    5.622423e+01                   2.753039e+01                7.773062e+01                       2.084047e+01
CFH                                      1.080379e+01                       5.342473e-01                    8.032033e+00                   1.131386e+00                9.253645e-01                       2.244359e+00
FUCA2                                    5.401895e+00                       1.856509e+01                    2.868583e+01                   7.919701e+00                9.253645e+00                       1.811518e+01
                          X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6                                       5.356113e+00                   9.311914e+00                6.753413e+00                       1.242409e+01                    4.302415e+00                   9.320130e+00
TNMD                                         4.057661e-01                   1.506339e+00                0.000000e+00                       1.104363e+00                    0.000000e+00                   3.535222e+00
DPM1                                         1.217298e+01                   1.163989e+01                1.000506e+01                       1.426469e+01                    1.916530e+01                   1.339099e+01
SCYL3                                        2.109984e+00                   4.108197e-01                3.751896e+00                       2.484817e+00                    5.475801e+00                   3.535222e+00
C1orf112                                     4.869193e-01                   2.738798e-01                2.501264e-01                       7.362421e-01                    4.302415e+00                   8.570235e-01
FGR                                          6.029684e+01                   2.998984e+01                3.576808e+01                       1.546109e+01                    3.441932e+01                   2.228261e+01
CFH                                          3.164976e+00                   2.191039e+00                3.001517e+00                       2.392787e+00                    7.040316e+00                   4.070862e+00
FUCA2                                        1.671756e+01                   1.999323e+01                2.976504e+01                       1.794590e+01                    1.486289e+01                   1.649770e+01
                          X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6                                   3.324255e+00                       7.937026e+00                    1.962340e+01                   7.050759e+00                1.610544e+01                       1.010132e+01
TNMD                                     0.000000e+00                       9.643116e-01                    0.000000e+00                   0.000000e+00                0.000000e+00                       0.000000e+00
DPM1                                     1.007350e+01                       1.973130e+01                    8.176417e+00                   8.973693e+00                1.030748e+01                       1.366649e+01
SCYL3                                    4.029399e+00                       3.263824e+00                    9.811700e+00                   2.435717e+00                2.576871e+00                       1.128971e+01
C1orf112                                 6.044099e-01                       6.676003e-01                    0.000000e+00                   1.153761e+00                1.288436e+00                       0.000000e+00
FGR                                      4.533074e+01                       4.331984e+01                    8.421709e+01                   4.595813e+01                6.012699e+01                       2.673878e+01
CFH                                      5.338954e+00                       2.225334e+00                    8.176417e-01                   1.666543e+00                2.147393e-01                       1.188390e+00
FUCA2                                    1.017423e+01                       1.142338e+01                    2.943510e+01                   1.166580e+01                2.405080e+01                       1.663746e+01
                          X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6                                       1.515445e+00                   2.090730e+00                       2.471578e+01                    1.362647e+01                5.996059e+00                      1.432008e+00
TNMD                                         0.000000e+00                   0.000000e+00                       0.000000e+00                    0.000000e+00                0.000000e+00                      0.000000e+00
DPM1                                         1.262871e+01                   3.484550e+00                       1.520971e+01                    1.132046e+01                9.593694e+00                      8.950050e+00
SCYL3                                        2.020593e+00                   4.181460e+00                       5.228339e+00                    3.354209e+00                5.036689e+00                      0.000000e+00
C1orf112                                     0.000000e+00                   0.000000e+00                       4.753035e-01                    1.257828e+00                0.000000e+00                      0.000000e+00
FGR                                          6.819501e+01                   1.404274e+02                       2.519109e+01                    4.402399e+01                4.485052e+01                      1.059686e+02
CFH                                          9.597816e+00                   1.393820e+00                       4.753035e+00                    5.031313e+00                3.117951e+00                      2.506014e+00
FUCA2                                        5.051482e+00                   3.519395e+01                       1.378380e+01                    1.299756e+01                2.518345e+01                      1.217207e+01
                          X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet
TSPAN6                                      9.936018e+00               7.383362e+00                     5.878601e+00                  3.639067e+00                 4.969456e+00              3.750479e+00
TNMD                                        0.000000e+00               0.000000e+00                     9.797668e-01                  0.000000e+00                 1.242364e+00              0.000000e+00
DPM1                                        2.692340e+01               3.164298e+01                     1.312887e+01                  1.637580e+01                 1.568485e+01              2.488954e+01
SCYL3                                       1.923100e+00               1.054766e+00                     5.878601e+00                  9.097668e+00                 3.105910e-01              3.409526e-01
C1orf112                                    0.000000e+00               0.000000e+00                     1.175720e+00                  6.368368e+00                 1.242364e+00              0.000000e+00
FGR                                         1.233989e+02               9.703847e+01                     9.033450e+01                  2.183440e+02                 8.153014e+01              2.557145e+02
CFH                                         1.282067e+01               1.054766e+01                     5.878601e+00                  5.458601e+00                 6.211820e+00              3.409526e-01
FUCA2                                       1.923100e+01               0.000000e+00                     1.548032e+01                  2.729300e+00                 8.230662e+00              1.363811e+01
                          X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet
TSPAN6                                        4.835611e+00                  1.588181e+00                 1.121909e+00              7.915673e-01                     0.000000e+00                  0.000000e+00
TNMD                                          0.000000e+00                  0.000000e+00                 9.349240e-02              0.000000e+00                     4.182015e-01                  0.000000e+00
DPM1                                          1.257259e+01                  9.869409e+00                 4.768112e+00              1.675484e+01                     1.087324e+01                  9.276729e-01
SCYL3                                         1.796084e+00                  4.537659e+00                 1.869848e+00              5.013260e+00                     4.600217e+00                  1.298742e+01
C1orf112                                      3.454008e+00                  4.537659e+00                 1.495878e+00              4.221692e+00                     0.000000e+00                  0.000000e+00
FGR                                           1.388511e+02                  4.116791e+02                 5.416950e+02              4.432777e+02                     9.493175e+01                  1.363679e+02
CFH                                           1.381603e+00                  3.403244e-01                 1.963340e+00              1.055423e+00                     1.881907e+00                  0.000000e+00
FUCA2                                         1.575028e+01                  1.134415e+01                 1.879197e+01              8.179529e+00                     2.195558e+01                  2.783019e+00
                          X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet
TSPAN6                                    7.206997e+00              0.000000e+00                     0.000000e+00                  0.000000e+00                 2.810612e+00              2.263747e-01
TNMD                                      3.603499e-01              0.000000e+00                     0.000000e+00                  0.000000e+00                 3.513265e-01              0.000000e+00
DPM1                                      6.846648e+00              6.110164e+00                     5.749153e+00                  4.865723e+00                 7.377856e+00              1.478982e+01
SCYL3                                     3.963849e+00              6.110164e+00                     2.555179e+00                  0.000000e+00                 1.405306e+00              3.546537e+00
C1orf112                                  0.000000e+00              8.146886e+00                     4.471564e+00                  9.731446e+00                 1.053979e+00              1.358248e+00
FGR                                       3.603499e+01              7.230361e+01                     4.222434e+02                  6.874571e+02                 4.138626e+02              3.418258e+02
CFH                                       0.000000e+00              3.055082e+00                     0.000000e+00                  6.951033e-01                 0.000000e+00              2.263747e-01
FUCA2                                     2.053994e+01              1.272951e+01                     8.943127e+00                  6.255929e+00                 1.774199e+01              1.305428e+01
                          X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6                                        6.214414e+00                  7.803588e-01                 2.135330e+00              6.634222e-01                     3.524965e+00                 2.697025e+00
TNMD                                          0.000000e+00                  1.418834e-01                 2.669162e-01              0.000000e+00                     4.699953e-01                 0.000000e+00
DPM1                                          1.118595e+01                  2.014745e+01                 2.162021e+01              3.980533e+00                     1.315987e+01                 1.449651e+01
SCYL3                                         5.592973e+00                  3.192377e+00                 2.135330e+00              1.149932e+01                     1.010490e+01                 3.371282e-01
C1orf112                                      0.000000e+00                  3.759911e+00                 2.402246e+00              2.211407e-01                     4.699953e-01                 2.022769e+00
FGR                                           1.938897e+02                  3.742175e+02                 6.459372e+01              4.842982e+01                     1.069239e+01                 1.955343e+01
CFH                                           0.000000e+00                  3.547086e-01                 1.601497e+00              7.518784e+00                     1.527485e+00                 8.428205e+00
FUCA2                                         2.299333e+01                  1.518153e+01                 1.521422e+01              1.437415e+01                     1.433486e+01                 2.056482e+01
                          X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6                                 0.000000e+00                     3.688823e+00                  1.052198e+00                 3.424994e+00              2.131069e+00                  0.000000e+00
TNMD                                   0.000000e+00                     3.882972e-01                  0.000000e+00                 0.000000e+00              0.000000e+00                  0.000000e+00
DPM1                                   1.190837e+00                     1.155184e+01                  7.966645e+00                 1.168527e+01              1.150777e+01                  2.033724e+01
SCYL3                                  9.526693e+00                     3.397600e+00                  1.202513e+00                 3.357837e+00              2.273140e+00                  0.000000e+00
C1orf112                               0.000000e+00                     3.980046e+00                  5.411306e+00                 2.686270e+00              3.693852e+00                  0.000000e+00
FGR                                    3.036633e+01                     1.446407e+02                  1.832328e+02                 2.197369e+02              3.423917e+02                  1.110726e+02
CFH                                    4.167928e+00                     1.164891e+00                  1.052198e+00                 1.477448e+00              0.000000e+00                  0.000000e+00
FUCA2                                  2.619841e+01                     2.164757e+01                  1.037167e+01                 1.202106e+01              1.747476e+01                  7.822014e+00
                          X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet
TSPAN6                                    8.878739e+00              2.318747e+00                     9.320149e-02                  6.223297e-01                 1.286401e+00              7.309524e-01
TNMD                                      0.000000e+00              0.000000e+00                     0.000000e+00                  0.000000e+00                 0.000000e+00              0.000000e+00
DPM1                                      1.161066e+01              9.274989e+00                     1.071817e+01                  1.397413e+01                 6.655729e+00              8.527777e+00
SCYL3                                     3.688092e+00              1.159374e+01                     2.423239e+00                  3.960280e+00                 4.977814e+00              5.360317e+00
C1orf112                                  8.195759e-01              7.729158e-01                     1.770828e+00                  3.677403e+00                 3.076177e+00              4.629365e+00
FGR                                       2.786558e+01              2.705205e+01                     3.686119e+02                  2.232466e+02                 3.631008e+02              2.378032e+02
CFH                                       2.322132e+00              2.318747e+01                     0.000000e+00                  5.657543e-02                 5.033745e-01              1.705555e+00
FUCA2                                     1.502556e+01              2.318747e+01                     1.481904e+01                  1.239002e+01                 1.879265e+01              1.145159e+01
                          X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte
TSPAN6                                        2.488515e+00                  3.452583e-01                 3.034350e+00              9.298885e-01                     3.338082e+00                 0.000000e+00
TNMD                                          1.508191e-01                  0.000000e+00                 0.000000e+00              3.099628e-01                     0.000000e+00                 0.000000e+00
DPM1                                          9.350785e+00                  1.484611e+01                 1.181799e+01              1.100368e+01                     7.027541e+00                 5.749777e+00
SCYL3                                         3.695068e+00                  3.590687e+00                 4.311971e+00              3.874535e+00                     3.513770e+00                 4.791481e+00
C1orf112                                      1.809829e+00                  2.002498e+00                 2.954499e+00              1.394833e+00                     1.581197e+00                 1.437444e+00
FGR                                           1.322684e+02                  3.271668e+02                 1.001335e+02              3.234462e+02                     1.310636e+02                 1.269742e+02
CFH                                           1.357372e+00                  1.450085e+00                 3.593309e+00              2.169740e+00                     7.027541e-01                 0.000000e+00
FUCA2                                         1.938026e+01                  1.374128e+01                 1.357472e+01              1.053874e+01                     8.257361e+00                 1.006211e+01
                          X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte
TSPAN6                                      0.00000                     3.965551e+00                  0.000000e+00                 1.612206e+00              0.000000e+00                     7.310093e+00
TNMD                                        0.00000                     5.918733e-02                  0.000000e+00                 2.072836e+00              0.000000e+00                     0.000000e+00
DPM1                                        8.97128                     9.469973e+00                  1.141130e+01                 1.289765e+01              8.912964e+00                     1.993662e+00
SCYL3                                       0.00000                     4.202300e+00                  1.951934e+00                 7.139770e+00              3.183202e+00                     6.645539e+00
C1orf112                                    0.00000                     3.965551e+00                  3.903867e+00                 6.909454e-01              8.488538e-01                     0.000000e+00
FGR                                       174.93997                     2.002899e+02                  4.035998e+02                 1.584568e+02              3.637338e+02                     3.588591e+01
CFH                                        11.21410                     3.965551e+00                  0.000000e+00                 0.000000e+00              1.697708e+00                     0.000000e+00
FUCA2                                      10.09269                     1.917669e+01                  1.981963e+01                 1.289765e+01              1.676486e+01                     6.645539e-01
                          X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                                     3.074225e+00                 1.185821e+01              7.899248e+00                 3.686534e+00             9.056043e+00
TNMD                                       0.000000e+00                 0.000000e+00              0.000000e+00                 0.000000e+00             0.000000e+00
DPM1                                       1.048853e+01                 1.506313e+01              9.163127e+00                 1.622075e+01             2.150810e+01
SCYL3                                      4.882593e+00                 8.973781e+00              4.739549e+00                 2.506843e+00             1.132005e+00
C1orf112                                   5.425103e-01                 2.403691e+00              9.479097e-01                 4.423841e-01             1.981009e+00
FGR                                        1.495520e+02                 3.669636e+01              1.248081e+02                 9.228132e+02             4.301621e+01
CFH                                        3.797572e+00                 2.724184e+00              8.531187e+00                 5.898454e-01             8.490041e+00
FUCA2                                      9.946023e+00                 1.554387e+01              1.390268e+01                 1.061722e+01             2.688513e+01
 [ reached getOption("max.print") -- omitted 23496 rows ]

$bone_hip_vs_tibia$fit
An object of class "DGEGLM"
$coefficients
         (Intercept)  batchpellet grouptibia
TSPAN6     -12.72969 -0.256260356  1.1966817
TNMD       -15.03322 -1.813749224  0.9475336
DPM1       -11.46287  0.122429782  0.1902987
SCYL3      -12.37079  0.002562051 -0.1146220
C1orf112   -13.25280  0.470777685 -0.8890405
23499 more rows ...

$fitted.values
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6                         91.332666                      27.377600                  22.8796365                          26.292265                      24.1770894                          13.318326
TNMD                            1.159694                       2.174532                   0.2905135                           2.088327                       0.3069878                           1.057840
DPM1                          173.450396                      35.502804                  43.4508504                          34.095360                      45.9148508                          17.270977
SCYL3                          45.548739                      10.513496                  11.4103598                          10.096707                      12.0574158                           5.114479
C1orf112                       13.695423                       1.962532                   3.4308240                           1.884731                       3.6253783                           0.954709
         X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6                        18.649625                          39.752242                      41.324303                   34.839070                          21.480325                      77.7818197
TNMD                           1.481292                           3.157418                       3.282283                    0.442368                           1.706127                       0.9876322
DPM1                          24.184515                          51.550027                      53.588649                   66.163080                          27.855318                     147.7159051
SCYL3                          7.161795                          15.265583                      15.869283                   17.374678                           8.248835                      38.7907628
C1orf112                       1.336877                           2.849594                       2.962285                    5.224153                           1.539793                      11.6634602
         X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6                       10.3379384                  12.8872315                          35.006727                      62.2615782                      9.6594779                  4.80074018
TNMD                          0.8211158                   0.1636352                           2.780494                       0.7905644                      0.7672274                  0.06095725
DPM1                         13.4060617                  24.4742162                          45.396125                     118.2413245                     12.5262457                  9.11711353
SCYL3                         3.9699561                   6.4270230                          13.443219                      31.0506250                      3.7094150                  2.39418896
C1orf112                      0.7410633                   1.9324530                           2.509417                       9.3361848                      0.6924286                  0.71987570
         X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6                           137.159538                      76.1354449                      80.929651                  25.8500155                          60.265211                      164.600244
TNMD                              10.894228                       0.9667274                       6.428033                   0.3282297                           4.786710                        2.090006
DPM1                             177.866142                     144.5892652                     104.948187                  49.0919144                          78.150895                      312.593279
SCYL3                             52.671754                      37.9696952                      31.078456                  12.8917249                          23.142936                       82.088193
C1orf112                           9.832125                      11.4165847                       5.801350                   3.8762352                           4.320043                       24.681968
         X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6                        6.9496150                          43.617422                       14.074222                      26.966461                   5.4299171                          21.043539
TNMD                          0.5519900                           3.464419                        0.178707                       2.141876                   0.0689462                           1.671434
DPM1                          9.0121418                          56.562327                       26.728437                      34.969645                  10.3119870                          27.288902
SCYL3                         2.6687784                          16.749882                        7.018990                      10.355611                   2.7079673                           8.081101
C1orf112                      0.4981752                           3.126665                        2.110443                       1.933060                   0.8142214                           1.508482
         X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6                        25.4781770                      5.3819507                  4.64493958                          75.120182                      26.5940931                      20.703701
TNMD                           0.3235083                      0.4274745                  0.05897897                           5.966602                       0.3376777                       1.644442
DPM1                          48.3857537                      6.9792216                  8.82123172                          97.414567                      50.5049965                      26.848206
SCYL3                         12.7062844                      2.0667668                  2.31648926                          28.847514                      13.2628057                       7.950597
C1orf112                       3.8204777                      0.3857990                  0.69651325                           5.384904                       3.9878104                       1.484121
         X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6                     9.7925134                          73.294837                      6.58589606                      25.957701                   8.1663779                          61.064875
TNMD                       0.1243401                           5.821620                      0.08362421                       2.061753                   0.1036923                           4.850225
DPM1                      18.5970190                          95.047490                     12.50731342                      33.661502                  15.5088157                          79.187885
SCYL3                      4.8836485                          28.146549                      3.28446844                       9.968229                   4.0726744                          23.450021
C1orf112                   1.4683970                           5.254057                      0.98756158                       1.860748                   1.2245564                           4.377366
         X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6                         93.118622                      71.486766                  30.2122266                         106.371435                      19.3206923                      91.380382
TNMD                            1.182371                       5.678009                   0.3836188                           8.448809                       0.2453239                       7.258108
DPM1                          176.842116                      92.702815                  57.3762149                         137.940657                      36.6920389                     118.500516
SCYL3                          46.439417                      27.452217                  15.0672139                          40.848563                       9.6354700                      35.091726
C1orf112                       13.963229                       5.124447                   4.5303530                           7.625115                       2.8971568                       6.550498
         X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6                     75.017393                         131.971959                       9.2422837                      152.72584                  35.1909391                          16.475047
TNMD                        0.952531                          10.482192                       0.1173536                       12.13062                   0.4468358                           1.308570
DPM1                      142.465967                         171.138978                      17.5520745                      198.05226                  66.8313166                          21.364559
SCYL3                      37.412109                          50.679629                       4.6092420                       58.64950                  17.5501599                           6.326717
C1orf112                   11.248932                           9.460259                       1.3858895                       10.94798                   5.2769159                           1.180995
         X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6                        14.9597209                      28.093707                          20.596085                      36.0472527                  31.5076799                         27.344518
TNMD                           0.1899506                       2.231411                           1.635894                       0.4577088                   0.4000678                          2.171905
DPM1                          28.4100928                      36.431438                          26.708651                      68.4575468                  59.8364177                         35.459903
SCYL3                          7.4605992                      10.788494                           7.909271                      17.9772141                  15.7132726                         10.500792
C1orf112                       2.2432248                       2.013865                           1.476407                       5.4053209                   4.7246075                          1.960161
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6                       23.5771682                 7.16450497                        15.001620                    2.49429248                    18.929187                 6.6555416                         21.27686
TNMD                          0.2993703                 0.09097107                         1.316079                    0.03498145                     1.660641                 0.0933413                          1.86660
DPM1                         44.7755370                13.60615296                        53.540512                   13.03687876                    67.557928                34.7864131                         75.93673
SCYL3                        11.7582276                 3.57302791                        21.528253                    4.64853875                    27.164555                12.4037350                         30.53361
C1orf112                      3.5354195                 1.07432456                         8.832051                    3.07184100                    11.144366                 8.1966192                         12.52653
         X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6                      20.0034807                    31.442319                  17.20049                        14.058379                    2.44614735                    8.1576767                4.45662220
TNMD                         0.2805408                     2.758407                   0.24123                         1.233329                    0.03430623                    0.7156658                0.06250233
DPM1                       104.5518736                   112.217070                  89.90154                        50.174102                   12.78523939                   29.1146016               23.29335623
SCYL3                       37.2798923                    45.121673                  32.05605                        20.174644                    4.55881211                   11.7067708                8.30567432
C1orf112                    24.6352473                    18.511345                  21.18323                         8.276728                    3.01254797                    4.8027492                5.48854432
         X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte
TSPAN6                          9.2036370                    3.26458612                    16.734394                30.0725872                        4.7303217                    31.9871686                   11.0132605
TNMD                            0.8074269                    0.04578451                     1.468094                 0.4217559                        0.4149869                     0.4486072                    0.9661836
DPM1                           32.8476150                   17.06296027                    59.724752               157.1799122                       16.8824332                   167.1868245                   39.3061287
SCYL3                          13.2077885                    6.08411212                    24.014891                56.0453868                        6.7883044                    59.6135354                   15.8047102
C1orf112                        5.4185476                    4.02049463                     9.852204                37.0358357                        2.7849288                    39.3937347                    6.4839450
         X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6                  10.2614503                        25.018274                    8.7195848                3.81114315                        30.282146                    15.0965546                    43.772489
TNMD                     0.1439127                         2.194831                    0.7649615                0.05344975                         2.656626                     0.2117231                     3.840122
DPM1                    53.6333586                        89.289771                   31.1200413               19.91964119                       108.076436                    78.9049216                   156.223226
SCYL3                   19.1239598                        35.902772                   12.5131437                7.10271421                        43.456753                    28.1350002                    62.816230
C1orf112                12.6374689                        14.729254                    5.1335668                4.69360587                        17.828305                    18.5921322                    25.770607
         X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte
TSPAN6                  15.9724409                     2.9010746                    21.520529                 2.9359273                        31.540459                    40.1097168                    52.558403
TNMD                     0.2240071                     0.0406864                     1.887977                 0.0411752                         2.767017                     0.5625227                     4.610902
DPM1                    83.4829026                    15.1630002                    76.806381                15.3451645                       112.567330                   209.6408177                   187.579997
SCYL3                   29.7673634                     5.4066464                    30.883291                 5.4716005                        45.262510                    74.7512870                    75.424561
C1orf112                19.6708283                     3.5728127                    12.669992                 3.6157355                        18.569124                    49.3970430                    30.943225
         X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte
TSPAN6                   9.3134299                        38.982031                    32.8627028                    36.813643                29.2838277                        16.731985                    6.1350923
TNMD                     0.1306171                         3.419859                     0.4608862                     3.229628                 0.4106939                         1.467882                    0.5382262
DPM1                    48.6783556                       139.126168                   171.7629652                   131.387230               153.0573157                        59.716154                   21.8960343
SCYL3                   17.3571624                        55.941626                    61.2452425                    52.829855                54.5753993                        24.011434                    8.8042371
C1orf112                11.4699363                        22.950274                    40.4719971                    21.673658                36.0644405                         9.850786                    3.6119732
         X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet
TSPAN6                  2.02354574                        49.666336                    15.1131777                    12.763458                10.6931234                        4.4234451                    12.5484680
TNMD                    0.02837942                         4.357184                     0.2119562                     1.119727                 0.1499668                        0.3880649                     0.1759872
DPM1                   10.57643427                       177.258259                    78.9918053                    45.552553                55.8895776                       15.7871960                    65.5868780
SCYL3                   3.77122205                        71.274265                    28.1659802                    18.316352                19.9284562                        6.3479174                    23.3862069
C1orf112                2.49209378                        29.240550                    18.6126044                     7.514356                13.1690951                        2.6042583                    15.4540412
         X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                      18.344396                 7.1817741                    15.388604                8.0184227
TNMD                         1.609338                 0.1007215                     0.215819                0.1124552
DPM1                        65.470819                37.5368644                    80.431373               41.9097622
SCYL3                       26.325343                13.3844590                    28.679285               14.9436961
C1orf112                    10.800076                 8.8446998                    18.951806                9.8750727
23499 more rows ...

$deviance
[1] 163.11534  57.67103  60.54948  81.65890  96.77025
23499 more elements ...

$iter
[1] 7 6 3 3 5
23499 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
23499 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6                                 3                             18                          28                                 12                              17                                 26
TNMD                                   0                              0                           0                                  0                               1                                 10
DPM1                                 177                             29                          42                                 33                              57                                  6
SCYL3                                 61                             26                          10                                 26                               7                                 14
C1orf112                              71                              0                           0                                  0                               9                                  0
         X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6                                9                                 43                             45                          33                                 16                              75
TNMD                                  3                                  4                              0                           0                                  0                               0
DPM1                                 19                                 70                             62                          33                                 34                             153
SCYL3                                 6                                 10                             13                          30                                  4                              24
C1orf112                              0                                  1                             22                           0                                  0                               6
         X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6                                5                           6                                 28                               4                              3                           9
TNMD                                  0                           0                                  0                               0                              0                           0
DPM1                                  6                          23                                 38                             159                             13                          19
SCYL3                                 5                           6                                  8                              16                              0                           7
C1orf112                              0                           0                                  2                              23                              0                           0
         X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6                                   65                              26                             62                          22                                 33                              17
TNMD                                      1                               0                              0                           7                                  3                               0
DPM1                                    174                             218                            105                          45                                101                             356
SCYL3                                    50                              38                             31                          19                                 18                              37
C1orf112                                 16                              37                             14                           4                                 19                              75
         X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6                                7                                 59                              15                             33                           7                                  4
TNMD                                  0                                 13                               0                              0                           0                                  0
DPM1                                 16                                 66                              20                             27                           0                                 26
SCYL3                                 2                                 12                               4                             21                           1                                 11
C1orf112                              0                                  0                               0                              2                           0                                  0
         X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6                                42                              0                          30                                 43                              29                             16
TNMD                                   0                              0                           0                                  0                               0                              0
DPM1                                  48                             15                           3                                 96                              45                             28
SCYL3                                 23                              0                           4                                 21                               0                              1
C1orf112                               4                              0                           0                                  3                               3                              0
         X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6                             5                                 75                              26                              7                          16                                 66
TNMD                               0                                 12                               0                              0                           0                                  8
DPM1                              16                                 59                              12                             26                          22                                 79
SCYL3                              1                                 38                               4                              5                           1                                 36
C1orf112                           0                                 10                               1                              0                           1                                  2
         X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6                                66                             68                          27                                135                              11                             87
TNMD                                   5                             11                           0                                 12                               0                             33
DPM1                                 150                             85                          40                                155                              49                            125
SCYL3                                 26                              3                          15                                 27                              14                             33
C1orf112                               6                              2                           1                                  8                              11                              8
         X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6                            33                                107                              24                            110                          75                                 17
TNMD                               0                                 13                               0                              0                           0                                  0
DPM1                             100                                266                              10                            140                          48                                 23
SCYL3                             40                                 44                              12                             38                          12                                 19
C1orf112                           6                                  9                               0                             18                           6                                  0
         X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6                                 3                              6                                 52                              65                          25                                 4
TNMD                                   0                              0                                  0                               0                           0                                 0
DPM1                                  25                             10                                 32                              54                          40                                25
SCYL3                                  4                             12                                 11                              16                          21                                 0
C1orf112                               0                              0                                  1                               6                           0                                 0
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6                               31                          7                               30                             4                           32                        11                               35
TNMD                                  0                          0                                5                             0                            8                         0                                0
DPM1                                 84                         30                               67                            18                          101                        73                               91
SCYL3                                 6                          1                               30                            10                            2                         1                               13
C1orf112                              0                          0                                6                             7                            8                         0                               25
         X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6                              14                           12                         6                                0                             0                           20                         0
TNMD                                 0                            1                         0                                2                             0                            1                         0
DPM1                                87                           51                       127                               52                             1                           19                        12
SCYL3                               40                           20                        38                               22                            14                           11                        12
C1orf112                            40                           16                        32                                0                             0                            0                        16
         X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte
TSPAN6                                  0                             0                           16                         3                               10                            11                            8
TNMD                                    0                             0                            2                         0                                0                             2                            1
DPM1                                   18                             7                           42                       196                               18                           284                           81
SCYL3                                   8                             0                            8                        47                                9                            45                            8
C1orf112                               14                            14                            6                        18                                0                            53                            9
         X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6                           3                               30                            8                         0                               38                             7                           51
TNMD                             0                                4                            0                         0                                4                             0                            0
DPM1                            18                              112                           43                         2                              119                            53                          174
SCYL3                           52                               86                            1                        16                               35                             8                           50
C1orf112                         1                                4                            6                         0                               41                            36                           40
         X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte
TSPAN6                          15                             0                           65                         3                                1                            11                           23
TNMD                             0                             0                            0                         0                                0                             0                            0
DPM1                            81                            26                           85                        12                              115                           247                          119
SCYL3                           16                             0                           27                        15                               26                            70                           89
C1orf112                        26                             0                            6                         1                               19                            65                           55
         X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte
TSPAN6                           3                               33                             5                           38                        12                               19                            0
TNMD                             0                                2                             0                            0                         4                                0                            0
DPM1                            35                              124                           215                          148                       142                               40                           12
SCYL3                           22                               49                            52                           54                        50                               20                           10
C1orf112                        19                               24                            29                           37                        18                                9                            3
         X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet
TSPAN6                           0                               67                             0                            7                         0                               11                            17
TNMD                             0                                1                             0                            9                         0                                0                             0
DPM1                             8                              160                            76                           56                        42                                3                            58
SCYL3                            0                               71                            13                           31                        15                               10                            27
C1orf112                         0                               67                            26                            3                         4                                0                             3
         X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                             74                        25                           25                       32
TNMD                                0                         0                            0                        0
DPM1                               94                        29                          110                       76
SCYL3                              56                        15                           17                        4
C1orf112                           15                         3                            3                        7
23499 more rows ...

$unshrunk.coefficients
         (Intercept)  batchpellet grouptibia
TSPAN6     -12.73723 -0.258841422  1.2030198
TNMD       -15.17073 -2.092282454  1.1036096
DPM1       -11.46495  0.122655226  0.1906258
SCYL3      -12.37602  0.002498425 -0.1152536
C1orf112   -13.26700  0.479201439 -0.9026990
23499 more rows ...

$df.residual
[1] 110 110 110 110 110
23499 more elements ...

$design
                                   (Intercept) batchpellet grouptibia
X102_tibia_non.sclerotic_pellet              1           1          1
X102_tibia_sclerotic_adipocyte               1           0          1
X102_tibia_sclerotic_pellet                  1           1          1
X104_tibia_non.sclerotic_adipocyte           1           0          1
X104_tibia_non.sclerotic_pellet              1           1          1
108 more rows ...

$offset
         [,1]     [,2]    [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]   [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 16.30756 14.84394 14.9233 14.80349 14.97846 14.12335 14.46004 15.21688 15.25566 15.34379 14.60135 16.14696 13.87003 14.34929 15.08975 15.9244 13.80215 13.36182 16.45536 16.12557 15.92779 15.04536 15.63297 16.89657
       [,25]    [,26]   [,27]    [,28]    [,29]   [,30]    [,31]    [,32]    [,33]   [,34]    [,35]    [,36]    [,37]   [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]   [,45]    [,46]    [,47]    [,48]
[1,] 13.4729 15.30967 14.4374 14.82881 13.48498 14.5808 15.03087 13.21726 13.32883 15.8533 15.07374 14.56452 14.07467 15.8287 13.67798 14.79068 13.89308 15.64615 16.32693 15.80372 15.2013 16.20115 14.75423 16.04924
        [,49]   [,50]    [,51]    [,52]    [,53]    [,54]    [,55]    [,56]    [,57]    [,58]    [,59]    [,60]    [,61]    [,62]    [,63]    [,64]    [,65]    [,66]    [,67]    [,68]    [,69]    [,70]    [,71]    [,72]
[1,] 16.11077 16.4168 14.01684 16.56286 15.35384 14.33606 14.49841 14.86976 14.55931 15.37788 15.24328 14.84273 14.95333 13.76219 15.44539 13.91008 15.67794 14.89152 15.79485 15.99198 16.18539 15.84101 15.38045 13.89059
        [,73]    [,74]    [,75]    [,76]   [,77]    [,78]    [,79]    [,80]    [,81]    [,82]    [,83]   [,84]  [,85]    [,86]    [,87]    [,88]    [,89]    [,90]    [,91]   [,92]   [,93]    [,94]    [,95]    [,96]
[1,] 14.83619 14.49046 14.95683 14.17921 15.5547 16.39969 14.29122 16.46141 15.13633 15.32447 15.95684 14.9028 14.334 16.14779 15.71054 16.51624 15.76694 14.06115 15.80624 14.0731 16.1885 16.68769 16.69916 15.22753
        [,97]    [,98]   [,99]   [,100]   [,101]   [,102]   [,103]   [,104]   [,105]   [,106]   [,107]   [,108]   [,109]   [,110]   [,111]  [,112]   [,113]
[1,] 16.40033 16.48841 16.3431 16.37311 15.55455 14.55126 13.70092 16.64256 15.71164 15.28382 15.36567 14.22415 15.52567 15.64656 14.96762 15.7297 15.07781
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]   5 113
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23499 more rows ...

$dispersion
[1] 0.6344835 5.7890991 0.4022576 0.8318417 1.7506890
23499 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  2.6271853 -0.6012498  3.6772455  2.1131351  0.9287606
23499 more elements ...

$df.residual.zeros
[1] 110 110 110 110 110
23499 more elements ...

$df.prior
[1] 13.36577 13.36577 13.36577 13.36577 13.36577
23499 more elements ...

$var.post
[1] 1.4305485 0.5396419 0.5795783 0.7766234 0.8972329
23499 more elements ...

$var.prior
[1] 0.9999703 0.6660528 0.8193053 1.0586628 1.0412855
23499 more elements ...

$samples
108 more rows ...

$genes
23499 more rows ...


$bone_hip_vs_tibia$mds_plot
$bone_hip_vs_tibia$mds_plot$rect
$bone_hip_vs_tibia$mds_plot$rect$w
[1] 0.8716978

$bone_hip_vs_tibia$mds_plot$rect$h
[1] 0.7661222

$bone_hip_vs_tibia$mds_plot$rect$left
[1] 3.131486

$bone_hip_vs_tibia$mds_plot$rect$top
[1] 1.929569


$bone_hip_vs_tibia$mds_plot$text
$bone_hip_vs_tibia$mds_plot$text$x
[1] 3.483424 3.483424

$bone_hip_vs_tibia$mds_plot$text$y
[1] 1.674194 1.418820



$bone_hip_vs_tibia$ql_disp_plot
NULL

$bone_hip_vs_tibia$boxplot_gg


$bone_non_sclerotic_hip_vs_tibia
$bone_non_sclerotic_hip_vs_tibia$name
[1] "tibia-vs-hip"

$bone_non_sclerotic_hip_vs_tibia$results
Coefficient:  grouptibia 

$bone_non_sclerotic_hip_vs_tibia$colsums_samples

$bone_non_sclerotic_hip_vs_tibia$normalized_matrix
                          X102_tibia_non.sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte
TSPAN6                                       2.544552e-01                       4.556620e+00                    5.441866e+00                       1.875811e+01                       1.016784e+01
TNMD                                         0.000000e+00                       0.000000e+00                    3.201097e-01                       7.214659e+00                       9.458457e-01
DPM1                                         1.501286e+01                       1.253071e+01                    1.824625e+01                       4.328795e+00                       1.655230e+01
SCYL3                                        5.173923e+00                       9.872678e+00                    2.240768e+00                       1.010052e+01                       2.364614e+00
C1orf112                                     6.022107e+00                       0.000000e+00                    2.880988e+00                       0.000000e+00                       2.364614e-01
FGR                                          1.133344e+03                       1.382175e+02                    1.213216e+02                       2.308691e+01                       4.043491e+01
CFH                                          7.633657e-01                       4.176902e+00                    1.600549e+00                       1.442932e+00                       4.256306e+00
FUCA2                                        1.170494e+01                       1.253071e+01                    6.082085e+00                       4.328795e+00                       1.205953e+01
GCLC                                         4.902504e+01                       2.771944e+01                    1.696582e+01                       6.132460e+01                       3.405045e+01
NFYA                                         5.776134e+01                       5.354029e+01                    3.969361e+01                       3.463036e+01                       2.080861e+01
STPG1                                        2.205279e+00                       3.797184e-01                    3.521207e+00                       7.214659e-01                       2.837537e+00
NIPAL3                                       1.781187e+01                       4.176902e+00                    5.121756e+00                       1.659371e+01                       3.310460e+00
LAS1L                                        5.046695e+01                       8.771494e+01                    7.394535e+01                       3.535183e+01                       4.800167e+01
ENPP4                                        1.314685e+01                       2.278310e+00                    3.201097e+00                       7.214659e-01                       6.384459e+00
SEMA3F                                       1.441913e+00                       8.771494e+01                    7.714645e+01                       4.978114e+01                       1.560645e+01
ANKIB1                                       7.718475e+00                       1.215099e+01                    1.280439e+01                       1.298639e+01                       1.418769e+01
CYP51A1                                      6.531018e+00                       6.834931e+00                    1.312450e+01                       5.050261e+00                       8.985535e+00
                          X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X144_Tibia_non.sclerotic_adipocyte
TSPAN6                                          7.355478e+00                    7.415489e+00                       8.034642e+00                    5.017895e-01                       4.775412e+00
TNMD                                            0.000000e+00                    0.000000e+00                       0.000000e+00                    0.000000e+00                       7.346787e-02
DPM1                                            1.563039e+01                    1.512760e+01                       1.090416e+01                    1.994613e+01                       1.278341e+01
SCYL3                                           1.838869e+00                    2.372957e+00                       2.295612e+00                    2.007158e+00                       3.673394e+00
C1orf112                                        0.000000e+00                    5.932391e-01                       5.739030e-01                    2.885290e+00                       1.175486e+00
FGR                                             3.861626e+01                    1.643272e+02                       2.321438e+02                    4.173635e+02                       2.347299e+02
CFH                                             1.838869e+00                    6.921123e-01                       1.147806e+00                    7.526843e-01                       1.836697e+00
FUCA2                                           2.068728e+01                    1.117267e+01                       1.147806e+01                    1.229384e+01                       1.572212e+01
GCLC                                            2.758304e+01                    2.847548e+01                       3.845150e+01                    6.335093e+01                       4.768065e+01
NFYA                                            1.700954e+01                    3.450674e+01                       2.812125e+01                    3.826145e+01                       3.173812e+01
STPG1                                           1.838869e+00                    5.141406e+00                       7.173788e+00                    3.888869e+00                       7.640659e+00
NIPAL3                                          1.287209e+01                    1.750055e+01                       1.836490e+01                    1.806442e+01                       1.564866e+01
LAS1L                                           3.631767e+01                    5.111744e+01                       3.012991e+01                    4.014316e+01                       3.680740e+01
ENPP4                                           2.298587e+00                    8.404221e+00                       1.492148e+01                    6.021474e+00                       2.791779e+00
SEMA3F                                          2.068728e+01                    6.051039e+01                       4.332968e+01                    2.998193e+01                       2.578722e+01
ANKIB1                                          1.471096e+01                    1.750055e+01                       1.262587e+01                    1.041213e+01                       1.234260e+01
CYP51A1                                         2.298587e+01                    7.316616e+00                       8.321594e+00                    7.777738e+00                       9.918163e+00
                          X144_Tibia_non.sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet
TSPAN6                                       2.661668e+00                       5.592374e+00                    8.147215e-01                       1.296000e+01                    8.290052e+00
TNMD                                         0.000000e+00                       5.083976e-01                    0.000000e+00                       2.855593e+00                    0.000000e+00
DPM1                                         2.231706e+01                       1.711605e+01                    1.706123e+01                       1.449762e+01                    1.105340e+01
SCYL3                                        3.890130e+00                       3.050386e+00                    1.773217e+00                       2.635932e+00                    2.210680e+00
C1orf112                                     3.787758e+00                       3.219852e+00                    3.594360e+00                       0.000000e+00                    0.000000e+00
FGR                                          3.589157e+02                       2.547072e+02                    6.406586e+02                       5.359728e+01                    1.348515e+02
CFH                                          4.094873e-01                       3.389317e-01                    2.875488e-01                       5.711185e+00                    7.737382e+00
FUCA2                                        1.883642e+01                       1.643819e+01                    9.584959e+00                       1.735322e+01                    6.632041e+00
GCLC                                         4.975271e+01                       7.541231e+01                    1.008817e+02                       3.514576e+01                    1.547476e+01
NFYA                                         3.900367e+01                       4.423059e+01                    5.147123e+01                       3.185084e+01                    6.079371e+00
STPG1                                        4.606733e+00                       9.320623e+00                    4.696630e+00                       5.271863e+00                    2.210680e+00
NIPAL3                                       1.863167e+01                       1.525193e+01                    1.888237e+01                       9.006100e+00                    8.842722e+00
LAS1L                                        4.862662e+01                       3.796035e+01                    5.818070e+01                       3.536542e+01                    3.260754e+01
ENPP4                                        8.087375e+00                       4.745044e+00                    3.019262e+00                       1.252068e+01                    2.210680e+00
SEMA3F                                       9.622953e+00                       4.948403e+01                    9.968357e+00                       2.789694e+01                    3.260754e+01
ANKIB1                                       7.370772e+00                       1.711605e+01                    8.243064e+00                       1.383864e+01                    6.632041e+00
CYP51A1                                      5.220964e+00                       1.508246e+01                    7.859666e+00                       1.164203e+01                    8.290052e+00
                          X151_Tibia_non.sclerotic_adipocyte X151_Tibia_non.sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte
TSPAN6                                          1.857733e+00                    1.274811e+01                       5.531746e+00                    8.579585e+00                       9.843050e+00
TNMD                                            0.000000e+00                    0.000000e+00                       0.000000e+00                    0.000000e+00                       1.574888e+00
DPM1                                            1.207527e+01                    1.456926e+01                       1.234994e+01                    1.331315e+01                       7.743200e+00
SCYL3                                           5.108767e+00                    6.981106e+00                       2.701550e+00                    0.000000e+00                       4.987145e+00
C1orf112                                        0.000000e+00                    1.214105e+00                       3.859358e-01                    8.875433e-01                       1.312407e+00
FGR                                             3.343920e+01                    5.524179e+01                       6.059192e+01                    1.399360e+02                       3.858476e+01
CFH                                             5.573200e+00                    3.035263e+00                       2.315615e+00                    1.183391e+00                       5.249627e-01
FUCA2                                           2.925930e+01                    1.608690e+01                       1.479420e+01                    7.396194e+00                       1.824245e+01
GCLC                                            2.925930e+01                    1.456926e+01                       3.910816e+01                    1.597578e+01                       3.320389e+01
NFYA                                            1.532630e+01                    4.461837e+01                       2.418531e+01                    1.804671e+01                       4.803409e+01
STPG1                                           1.253970e+01                    1.153400e+01                       6.174972e+00                    8.875433e+00                       9.843050e+00
NIPAL3                                          5.108767e+00                    8.498738e+00                       1.247859e+01                    2.337197e+01                       2.480449e+01
LAS1L                                           3.715467e+01                    2.944206e+01                       4.785604e+01                    4.526471e+01                       3.897848e+01
ENPP4                                           1.671960e+01                    8.498738e+00                       7.461425e+00                    5.916955e-01                       7.874440e+00
SEMA3F                                          1.904177e+01                    4.704658e+01                       1.698117e+01                    4.467301e+01                       3.451630e+01
ANKIB1                                          2.136393e+01                    1.031990e+01                       2.071189e+01                    1.627163e+01                       2.559193e+01
CYP51A1                                         1.857733e+00                    6.677580e+00                       8.747878e+00                    1.212976e+01                       8.924366e+00
                          X156_Tibia_non.sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte X159_Tibia_non.sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet
TSPAN6                                       3.127640e+01                       1.009487e+01                    5.524393e+00                       1.179132e+01                    4.367590e+00
TNMD                                         0.000000e+00                       1.223620e+00                    4.185146e-01                       1.048118e+00                    0.000000e+00
DPM1                                         1.443526e+01                       1.208325e+01                    1.255544e+01                       1.353819e+01                    1.945563e+01
SCYL3                                        4.811754e+00                       5.506291e+00                    2.176276e+00                       2.358265e+00                    5.558750e+00
C1orf112                                     1.202938e+00                       3.059050e-01                    5.022175e-01                       6.987451e-01                    4.367590e+00
FGR                                          5.894398e+01                       1.988383e+01                    6.219127e+01                       1.467365e+01                    3.494072e+01
CFH                                          8.420569e+00                       2.141335e+00                    3.264414e+00                       2.270922e+00                    7.146965e+00
FUCA2                                        3.007346e+01                       1.728363e+01                    1.724280e+01                       1.703191e+01                    1.508804e+01
GCLC                                         2.165289e+01                       3.426136e+01                    2.552939e+01                       3.878035e+01                    2.620554e+01
NFYA                                         4.571166e+01                       2.860212e+01                    2.954713e+01                       3.397648e+01                    3.295545e+01
STPG1                                        0.000000e+00                       3.823813e+00                    4.268849e+00                       8.559628e+00                    5.955804e+00
NIPAL3                                       2.044995e+01                       8.871246e+00                    1.322506e+01                       1.013180e+01                    4.764643e+00
LAS1L                                        2.285583e+01                       4.053242e+01                    3.599226e+01                       3.825629e+01                    2.580848e+01
ENPP4                                        0.000000e+00                       6.882863e+00                    5.105878e+00                       6.288706e+00                    1.270572e+01
SEMA3F                                       5.894398e+01                       2.753145e+01                    4.461366e+01                       2.183578e+01                    4.685233e+01
ANKIB1                                       4.811754e+00                       2.630783e+01                    1.799613e+01                       2.681434e+01                    1.548509e+01
CYP51A1                                      7.217630e+00                       1.147144e+01                    1.657318e+01                       1.537239e+01                    1.985268e+01
                          X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_adipocyte
TSPAN6                                          7.842766e+00                    2.026926e+01                       1.019627e+01                    1.594616e+00                       2.398367e+01
TNMD                                            9.528594e-01                    0.000000e+00                       0.000000e+00                    0.000000e+00                       0.000000e+00
DPM1                                            1.949697e+01                    8.445525e+00                       1.379496e+01                    1.328846e+01                       1.475918e+01
SCYL3                                           3.225062e+00                    1.013463e+01                       1.139583e+01                    2.126154e+00                       5.073468e+00
C1orf112                                        6.596719e-01                    0.000000e+00                       0.000000e+00                    0.000000e+00                       4.612244e-01
FGR                                             4.280537e+01                    8.698891e+01                       2.699014e+01                    7.175770e+01                       2.444489e+01
CFH                                             2.198906e+00                    8.445525e-01                       1.199562e+00                    1.009923e+01                       4.612244e+00
FUCA2                                           1.128772e+01                    3.040389e+01                       1.679386e+01                    5.315385e+00                       1.337551e+01
GCLC                                            2.631358e+01                    3.040389e+01                       2.339145e+01                    8.504616e+00                       1.522040e+01
NFYA                                            4.104625e+01                    2.280292e+01                       1.379496e+01                    1.647769e+01                       2.121632e+01
STPG1                                           4.764297e+00                    1.942471e+01                       7.797150e+00                    3.189231e+00                       9.685712e+00
NIPAL3                                          1.209398e+01                    1.604650e+01                       5.997808e+00                    3.295539e+01                       1.706530e+01
LAS1L                                           3.928712e+01                    3.969397e+01                       2.818970e+01                    2.976616e+01                       3.228571e+01
ENPP4                                           5.277375e+00                    0.000000e+00                       3.598685e+00                    5.846924e+00                       2.306122e+00
SEMA3F                                          3.408305e+01                    4.391673e+01                       1.199562e+01                    3.189231e+01                       2.767346e+00
ANKIB1                                          1.839752e+01                    1.858016e+01                       5.398027e+00                    1.116231e+01                       2.859591e+01
CYP51A1                                         1.458608e+01                    1.942471e+01                       3.598685e+00                    1.435154e+01                       5.073468e+00
                          X164_tibia_non.sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6                                       1.402975e+01                      1.401284e+00                   1.024725e+01                     6.013240e+00                  3.704418e+00                     5.042266e+00
TNMD                                         0.000000e+00                      0.000000e+00                   0.000000e+00                     1.002207e+00                  0.000000e+00                     0.000000e+00
DPM1                                         1.165548e+01                      8.758023e+00                   2.776673e+01                     1.342957e+01                  1.666988e+01                     1.310989e+01
SCYL3                                        3.453476e+00                      0.000000e+00                   1.983338e+00                     6.013240e+00                  9.261044e+00                     1.872842e+00
C1orf112                                     1.295053e+00                      0.000000e+00                   0.000000e+00                     1.202648e+00                  6.482731e+00                     3.601619e+00
FGR                                          4.532687e+01                      1.036950e+02                   1.272642e+02                     9.240345e+01                  2.222651e+02                     1.447851e+02
CFH                                          5.180214e+00                      2.452246e+00                   1.322225e+01                     6.013240e+00                  5.556626e+00                     1.440647e+00
FUCA2                                        1.338222e+01                      1.191091e+01                   1.983338e+01                     1.583486e+01                  2.778313e+00                     1.642338e+01
GCLC                                         1.769906e+01                      3.257985e+01                   1.388337e+01                     3.928650e+01                  2.222651e+01                     6.165971e+01
NFYA                                         2.935454e+01                      3.608306e+01                   1.751949e+01                     3.267194e+01                  3.611807e+01                     3.875342e+01
STPG1                                        5.396056e+00                      7.006418e-01                   0.000000e+00                     1.182604e+01                  2.778313e+00                     3.889748e+00
NIPAL3                                       1.489311e+01                      1.646508e+01                   1.553615e+01                     7.817212e+00                  9.261044e+00                     1.872842e+01
LAS1L                                        4.252092e+01                      4.764365e+01                   3.867509e+01                     6.333946e+01                  5.834458e+01                     6.410881e+01
ENPP4                                        1.942580e+00                      8.057381e+00                   3.636120e+00                     3.207061e+00                  7.408835e+00                     8.643885e-01
SEMA3F                                       4.295260e+01                      2.136958e+01                   4.131954e+01                     5.612357e+01                  3.704418e+01                     2.650791e+01
ANKIB1                                       1.359806e+01                      1.751605e+01                   8.594465e+00                     2.806179e+01                  8.334939e+00                     3.010953e+01
CYP51A1                                      1.165548e+01                      1.646508e+01                   2.247783e+01                     1.022251e+01                  8.334939e+00                     1.181331e+01
                          X125_Hip_non.sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X143_Hip_non.sclerotic_adipocyte
TSPAN6                                     1.680567e+00                     0.000000e+00                  0.000000e+00                     0.000000e+00                  0.000000e+00                     6.789262e+00
TNMD                                       0.000000e+00                     4.296881e-01                  0.000000e+00                     0.000000e+00                  0.000000e+00                     0.000000e+00
DPM1                                       1.044353e+01                     1.117189e+01                  9.507294e-01                     6.034610e+00                  4.975036e+00                     1.222067e+01
SCYL3                                      4.801621e+00                     4.726569e+00                  1.331021e+01                     2.682049e+00                  0.000000e+00                     6.110336e+00
C1orf112                                   4.801621e+00                     0.000000e+00                  0.000000e+00                     4.693586e+00                  9.950072e+00                     0.000000e+00
FGR                                        4.356271e+02                     9.753920e+01                  1.397572e+02                     4.432086e+02                  7.029015e+02                     2.118250e+02
CFH                                        3.601216e-01                     1.933597e+00                  0.000000e+00                     0.000000e+00                  7.107194e-01                     0.000000e+00
FUCA2                                      1.200405e+01                     2.255863e+01                  2.852188e+00                     9.387171e+00                  6.396475e+00                     2.512027e+01
GCLC                                       8.354821e+01                     2.341800e+01                  1.045802e+01                     5.431149e+01                  5.970043e+01                     4.956161e+01
NFYA                                       7.502533e+01                     4.125006e+01                  2.376823e+01                     2.916728e+01                  4.122173e+01                     2.647812e+01
STPG1                                      5.761946e+00                     2.363285e+00                  4.753647e+00                     4.693586e+00                  1.350367e+01                     9.504966e+00
NIPAL3                                     1.752592e+01                     1.289064e+01                  3.232480e+01                     1.978011e+01                  1.421439e+01                     1.833101e+01
LAS1L                                      6.566217e+01                     4.167975e+01                  5.133939e+01                     6.135187e+01                  5.898971e+01                     3.598309e+01
ENPP4                                      3.121054e+00                     6.015634e+00                  0.000000e+00                     0.000000e+00                  1.421439e+00                     1.561530e+01
SEMA3F                                     1.920649e+00                     1.160158e+01                  3.897990e+01                     1.005768e+01                  2.132158e+00                     1.900993e+01
ANKIB1                                     1.860628e+01                     2.384769e+01                  2.471896e+01                     2.246216e+01                  7.817913e+00                     2.104671e+01
CYP51A1                                    6.002027e+00                     7.089854e+00                  7.605835e+00                     7.040379e+00                  7.107194e+00                     0.000000e+00
                          X143_Hip_non.sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X150_Hip_non.sclerotic_pellet X152_Hip_non.sclerotic_adipocyte
TSPAN6                                     8.379315e-01                     3.511316e+00                     4.013709e+00                  1.096754e+00                  0.000000e+00                     9.875994e-02
TNMD                                       1.523512e-01                     4.681755e-01                     4.224957e-01                  0.000000e+00                  0.000000e+00                     0.000000e+00
DPM1                                       2.163387e+01                     1.310891e+01                     1.256925e+01                  8.303995e+00                  2.140436e+01                     1.135739e+01
SCYL3                                      3.427902e+00                     1.006577e+01                     3.696837e+00                  1.253433e+00                  0.000000e+00                     2.567758e+00
C1orf112                                   4.037306e+00                     4.681755e-01                     4.330581e+00                  5.640450e+00                  0.000000e+00                     1.876439e+00
FGR                                        4.018262e+02                     1.065099e+01                     1.573797e+02                  1.909919e+02                  1.169007e+02                     3.905956e+02
CFH                                        3.808780e-01                     1.521570e+00                     1.267487e+00                  1.096754e+00                  0.000000e+00                     0.000000e+00
FUCA2                                      1.630158e+01                     1.427935e+01                     2.355414e+01                  1.081086e+01                  8.232445e+00                     1.570283e+01
GCLC                                       7.061477e+01                     3.686882e+01                     6.590933e+01                  7.003558e+01                  1.070218e+01                     9.362442e+01
NFYA                                       6.223546e+01                     3.359159e+01                     5.344571e+01                  3.775968e+01                  3.622276e+01                     6.873692e+01
STPG1                                      2.361443e+00                     1.346005e+01                     4.964325e+00                  5.953808e+00                  4.116223e+00                     4.049157e+00
NIPAL3                                     2.727086e+01                     2.177016e+01                     2.513849e+01                  2.553870e+01                  1.646489e+00                     3.624490e+01
LAS1L                                      4.920943e+01                     5.629811e+01                     4.489017e+01                  4.371349e+01                  4.692494e+01                     5.263905e+01
ENPP4                                      5.636994e+00                     4.213580e+00                     5.069949e+00                  1.723471e+00                  5.762712e+00                     4.147917e+00
SEMA3F                                     4.113482e+00                     3.019732e+01                     2.154728e+01                  1.519788e+01                  3.704600e+01                     7.011956e+00
ANKIB1                                     1.500659e+01                     3.874152e+01                     2.556099e+01                  1.535456e+01                  4.116223e+00                     1.106111e+01
CYP51A1                                    1.180722e+01                     5.852194e+00                     7.182427e+00                  6.423846e+00                  4.116223e+00                     3.654118e+00
                          X152_Hip_non.sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet
TSPAN6                                     6.608755e-01                     2.662070e+00                  3.699158e-01                     3.549722e+00                     4.308813e+00                  0.000000e+00
TNMD                                       0.000000e+00                     1.613376e-01                  0.000000e+00                     0.000000e+00                     6.431063e-02                  0.000000e+00
DPM1                                       1.483966e+01                     1.000293e+01                  1.590638e+01                     7.473099e+00                     1.028970e+01                  1.191379e+01
SCYL3                                      4.205571e+00                     3.952771e+00                  3.847124e+00                     3.736549e+00                     4.566055e+00                  2.037886e+00
C1orf112                                   3.905173e+00                     1.936051e+00                  2.145512e+00                     1.681447e+00                     4.308813e+00                  4.075771e+00
FGR                                        2.370741e+02                     1.414931e+02                  3.505322e+02                     1.393733e+02                     2.176272e+02                  4.213720e+02
CFH                                        6.007959e-02                     1.452038e+00                  1.553646e+00                     7.473099e-01                     4.308813e+00                  0.000000e+00
FUCA2                                      1.315743e+01                     2.073188e+01                  1.472265e+01                     8.780891e+00                     2.083665e+01                  2.069238e+01
GCLC                                       1.074223e+02                     7.106921e+01                  9.270090e+01                     6.389499e+01                     1.232835e+02                  6.552586e+01
NFYA                                       5.052693e+01                     4.017306e+01                  5.238008e+01                     3.867328e+01                     4.456727e+01                  3.636842e+01
STPG1                                      6.188198e+00                     7.744205e+00                  4.734922e+00                     7.473099e-01                     5.209161e+00                  3.291969e+00
NIPAL3                                     2.853780e+01                     3.025080e+01                  3.107293e+01                     3.045288e+01                     2.418080e+01                  2.414111e+01
LAS1L                                      7.119431e+01                     4.670724e+01                  6.051822e+01                     5.679555e+01                     5.222024e+01                  6.286093e+01
ENPP4                                      2.823741e+00                     4.840128e+00                  1.701613e+00                     2.428757e+00                     3.344153e+00                  2.978448e+00
SEMA3F                                     3.905173e+00                     2.290994e+01                  4.586956e+00                     3.699184e+01                     1.948612e+01                  2.351406e+00
ANKIB1                                     1.910531e+01                     2.484599e+01                  1.709011e+01                     2.858460e+01                     2.353769e+01                  1.724365e+01
CYP51A1                                    6.728914e+00                     1.048694e+01                  4.438989e+00                     2.055102e+00                     5.466404e+00                  1.065971e+01
                          X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X79_Hip_non.sclerotic_pellet
TSPAN6                                            7.497589                  3.230584e+00                 3.869183e+00
TNMD                                              0.000000                  0.000000e+00                 0.000000e+00
DPM1                                              2.044797                  1.102199e+01                 1.702441e+01
SCYL3                                             6.815990                  5.130928e+00                 2.631045e+00
C1orf112                                          0.000000                  5.701031e-01                 4.643020e-01
FGR                                              36.806347                  1.571584e+02                 9.685339e+02
CFH                                               0.000000                  3.990722e+00                 6.190693e-01
FUCA2                                             0.681599                  1.045189e+01                 1.114325e+01
GCLC                                             65.433507                  7.981444e+01                 4.426346e+01
NFYA                                              5.452792                  4.275773e+01                 5.710914e+01
STPG1                                             0.000000                  7.601375e+00                 4.952554e+00
NIPAL3                                           10.905584                  2.033368e+01                 2.089359e+01
LAS1L                                            54.527922                  3.382612e+01                 5.323996e+01
ENPP4                                             0.000000                  1.520275e+00                 3.869183e+00
SEMA3F                                           62.707110                  2.451443e+01                 1.470290e+01
ANKIB1                                           14.995179                  1.881340e+01                 9.595574e+00
CYP51A1                                          12.268782                  1.976357e+01                 1.036941e+01
 [ reached getOption("max.print") -- omitted 23208 rows ]

$bone_non_sclerotic_hip_vs_tibia$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) batchpellet grouptibia
TSPAN6     -12.76658  -0.4524918  1.3247510
TNMD       -15.05776  -2.2775275  1.1007186
DPM1       -11.47353   0.2197903  0.2142905
SCYL3      -12.23994  -0.2014172 -0.1076753
C1orf112   -13.24306   0.8728437 -0.9187555
23220 more rows ...

$fitted.values
         X102_tibia_non.sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte
TSPAN6                        80.1935126                          28.259036                      21.2486082                          14.873157                          45.379388                          23.341462
TNMD                           0.7264813                           2.343593                       0.1924933                           1.233468                           3.763426                           1.935766
DPM1                         189.0640639                          33.887326                      50.0956759                          17.835411                          54.417500                          27.990329
SCYL3                         41.5938606                          11.376114                      11.0209868                           5.987421                          18.268178                           9.396468
C1orf112                      19.6973367                           1.814149                       5.2191378                           0.954814                           2.913227                           1.498455
         X128_tibia_non.sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte
TSPAN6                        68.7940412                          37.394734                      54.2210293                         146.056704                      66.4429451                          63.319388
TNMD                           0.6232123                           3.101239                       0.4911939                          12.112848                       0.6019135                           5.251235
DPM1                         162.1886930                          44.842560                     127.8313896                         175.146492                     156.6457536                          75.930569
SCYL3                         35.6813122                          15.053832                      28.1227478                          58.797397                      34.4618724                          25.490204
C1orf112                      16.8973693                           2.400635                      13.3179086                           9.376421                      16.3198870                           4.064923
         X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte X151_Tibia_non.sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte
TSPAN6                        141.928339                          48.850168                      12.3073169                          23.104445                      22.4095422                          83.411354
TNMD                            1.285744                           4.051267                       0.1114933                           1.916109                       0.2030104                           6.917512
DPM1                          334.609967                          58.579547                      29.0157056                          27.706106                      52.8326914                         100.024208
SCYL3                          73.613780                          19.665395                       6.3834194                           9.301054                      11.6231269                          33.578537
C1orf112                       34.860804                           3.136041                       3.0229548                           1.483239                       5.5042894                           5.354770
         X155_Tibia_non.sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte X159_Tibia_non.sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte
TSPAN6                        22.9911699                          81.761814                      5.65439290                          70.155596                       81.262231                          122.85424
TNMD                           0.2082794                           6.780712                      0.05122373                           5.818179                        0.736163                           10.18861
DPM1                          54.2039358                          98.046132                     13.33078532                          84.128329                      191.583671                          147.32285
SCYL3                         11.9247989                          32.914489                      2.93275631                          28.242226                       42.148171                           49.45689
C1orf112                       5.6471503                           5.248874                      1.38884652                           4.503788                       19.959838                            7.88689
         X160_Tibia_non.sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_adipocyte
TSPAN6                        17.1309020                         146.397446                      8.05383443                          17.890662                      12.7966010                          23.265195
TNMD                           0.1551906                          12.141106                      0.07296052                           1.483717                       0.1159257                           1.929441
DPM1                          40.3877800                         175.555099                     18.98770384                          21.453905                      30.1692406                          27.898872
SCYL3                          8.8852617                          58.934568                      4.17727140                           7.202164                       6.6371957                           9.365766
C1orf112                       4.2077362                           9.398296                      1.97820352                           1.148529                       3.1431340                           1.493559
         X164_tibia_non.sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6                        31.5132316                         30.630415                      20.577086                        14.132433                    1.93889668                        19.662850
TNMD                           0.2854816                          2.540257                       0.186410                         1.219199                    0.01827143                         1.696305
DPM1                          74.2955313                         36.731006                      48.512497                        51.796839                   13.97110645                        72.066395
SCYL3                         16.3449251                         12.330750                      10.672690                        24.014607                    4.24489167                        33.412196
C1orf112                       7.7403610                          1.966385                       5.054197                         8.725846                    4.58034234                        12.140514
         X125_Hip_non.sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X143_Hip_non.sclerotic_adipocyte
TSPAN6                      14.9584532                        13.185022                    1.88867700                        8.4494312                    2.52648330                        4.1723587
TNMD                         0.1409628                         1.137466                    0.01779818                        0.7289286                    0.02380863                        0.3599475
DPM1                       107.7861160                        48.324478                   13.60923854                       30.9680462                   18.20507896                       15.2921295
SCYL3                       32.7490444                        22.404714                    4.13494403                       14.3577381                    5.53131481                        7.0899013
C1orf112                    35.3370231                         8.140882                    4.46170614                        5.2169671                    5.96842450                        2.5761566
         X143_Hip_non.sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X150_Hip_non.sclerotic_pellet X152_Hip_non.sclerotic_adipocyte
TSPAN6                      23.5721272                        24.202236                        26.818956                    11.4604948                    2.18115113                        28.682921
TNMD                         0.2221349                         2.087916                         2.313659                     0.1079994                    0.02055435                         2.474463
DPM1                       169.8536604                        88.703716                        98.294271                    82.5808797                   15.71671916                       105.125897
SCYL3                       51.6072503                        41.125769                        45.572245                    25.0908466                    4.77526747                        48.739597
C1orf112                    55.6854903                        14.943286                        16.558939                    27.0736395                    5.15263086                        17.709814
         X152_Hip_non.sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet
TSPAN6                      29.8873665                        35.115478                    24.2706687                        15.162244                        44.047513                    11.4545535
TNMD                         0.2816473                         3.029396                     0.2287177                         1.308040                         3.799959                     0.1079434
DPM1                       215.3593764                       128.701886                   174.8871408                        55.571203                       161.438727                    82.5380681
SCYL3                       65.4334162                        59.670151                    53.1365908                        25.764518                        74.847956                    25.0778390
C1orf112                    70.6042627                        21.681494                    57.3356862                         9.361687                        27.196437                    27.0596040
         X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X79_Hip_non.sclerotic_pellet
TSPAN6                           4.155997                    9.44892586                   11.6020659
TNMD                             0.358536                    0.08904313                    0.1093335
DPM1                            15.232162                   68.08611853                   83.6009980
SCYL3                            7.062099                   20.68685098                   25.4007928
C1orf112                         2.566054                   22.32162016                   27.4080791
23220 more rows ...

$deviance
[1] 90.06658 27.14808 21.87904 40.69051 54.05294
23220 more elements ...

$iter
[1] 7 6 3 4 6
23220 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
23220 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_non.sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte
TSPAN6                                 3                                 12                              17                                 26                                 43                                 16
TNMD                                   0                                  0                               1                                 10                                  4                                  0
DPM1                                 177                                 33                              57                                  6                                 70                                 34
SCYL3                                 61                                 26                               7                                 14                                 10                                  4
C1orf112                              71                                  0                               9                                  0                                  1                                  0
         X128_tibia_non.sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte
TSPAN6                                75                                 28                               4                                 65                              26                                 33
TNMD                                   0                                  0                               0                                  1                               0                                  3
DPM1                                 153                                 38                             159                                174                             218                                101
SCYL3                                 24                                  8                              16                                 50                              38                                 18
C1orf112                               6                                  2                              23                                 16                              37                                 19
         X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte X151_Tibia_non.sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte
TSPAN6                                17                                 59                              15                                  4                              42                                 43
TNMD                                   0                                 13                               0                                  0                               0                                  0
DPM1                                 356                                 66                              20                                 26                              48                                 96
SCYL3                                 37                                 12                               4                                 11                              23                                 21
C1orf112                              75                                  0                               0                                  0                               4                                  3
         X155_Tibia_non.sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte X159_Tibia_non.sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte
TSPAN6                                29                                 75                              26                                 66                              66                                135
TNMD                                   0                                 12                               0                                  8                               5                                 12
DPM1                                  45                                 59                              12                                 79                             150                                155
SCYL3                                  0                                 38                               4                                 36                              26                                 27
C1orf112                               3                                 10                               1                                  2                               6                                  8
         X160_Tibia_non.sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_adipocyte
TSPAN6                                11                                107                              24                                 17                               3                                 52
TNMD                                   0                                 13                               0                                  0                               0                                  0
DPM1                                  49                                266                              10                                 23                              25                                 32
SCYL3                                 14                                 44                              12                                 19                               4                                 11
C1orf112                              11                                  9                               0                                  0                               0                                  1
         X164_tibia_non.sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6                                65                                 4                             31                               30                             4                               35
TNMD                                   0                                 0                              0                                5                             0                                0
DPM1                                  54                                25                             84                               67                            18                               91
SCYL3                                 16                                 0                              6                               30                            10                               13
C1orf112                               6                                 0                              0                                6                             7                               25
         X125_Hip_non.sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X143_Hip_non.sclerotic_adipocyte
TSPAN6                              14                                0                             0                                0                             0                               10
TNMD                                 0                                2                             0                                0                             0                                0
DPM1                                87                               52                             1                               18                             7                               18
SCYL3                               40                               22                            14                                8                             0                                9
C1orf112                            40                                0                             0                               14                            14                                0
         X143_Hip_non.sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X150_Hip_non.sclerotic_pellet X152_Hip_non.sclerotic_adipocyte
TSPAN6                              11                               30                               38                             7                             0                                1
TNMD                                 2                                4                                4                             0                             0                                0
DPM1                               284                              112                              119                            53                            26                              115
SCYL3                               45                               86                               35                             8                             0                               26
C1orf112                            53                                4                               41                            36                             0                               19
         X152_Hip_non.sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet
TSPAN6                              11                               33                             5                               19                               67                             0
TNMD                                 0                                2                             0                                0                                1                             0
DPM1                               247                              124                           215                               40                              160                            76
SCYL3                               70                               49                            52                               20                               71                            13
C1orf112                            65                               24                            29                                9                               67                            26
         X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X79_Hip_non.sclerotic_pellet
TSPAN6                                 11                            17                           25
TNMD                                    0                             0                            0
DPM1                                    3                            58                          110
SCYL3                                  10                            27                           17
C1orf112                                0                             3                            3
23220 more rows ...

$unshrunk.coefficients
         (Intercept) batchpellet grouptibia
TSPAN6     -12.77427  -0.4558879  1.3318492
TNMD       -15.22455  -2.6701447  1.2923996
DPM1       -11.47542   0.2201276  0.2146202
SCYL3      -12.24408  -0.2024806 -0.1082380
C1orf112   -13.25645   0.8859497 -0.9317646
23220 more rows ...

$df.residual
[1] 54 54 54 54 54
23220 more elements ...

$design
                                   (Intercept) batchpellet grouptibia
X102_tibia_non.sclerotic_pellet              1           1          1
X104_tibia_non.sclerotic_adipocyte           1           0          1
X104_tibia_non.sclerotic_pellet              1           1          1
X105_tibia_non.sclerotic_adipocyte           1           0          1
X109_tibia_non.sclerotic_adipocyte           1           0          1
52 more rows ...

$offset
         [,1]     [,2]    [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]   [,15]    [,16]   [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 16.28275 14.78384 14.9546 14.14198 15.25748 14.59265 16.12943 15.06395 15.89138 16.42642 16.09465 15.59061 16.85363 15.33118 14.4085 14.58245 15.0078 15.86621 15.03342 15.84623 13.63074 15.69314 16.29599 16.25342
        [,25]    [,26]    [,27]   [,28]    [,29]    [,30]    [,31]    [,32]    [,33]    [,34]    [,35]  [,36]    [,37]    [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]
[1,] 14.73919 16.42875 13.98446 14.3267 14.44749 14.58938 15.34872 14.86442 14.92249 15.42274 13.89228 15.753 15.93544 15.35335 13.86604 14.90837 14.15699 14.20275 16.39022 15.96072 16.06338 15.66907 14.01001 16.13057
       [,49]    [,50]    [,51]    [,52]    [,53]    [,54]    [,55]    [,56]    [,57]
[1,] 16.6276 16.33291 16.41943 15.49308 16.55954 15.66855 14.19882 15.47606 15.68134
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 57
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23220 more rows ...

$dispersion
[1] 0.5889180 4.8757760 0.3757245 0.7618057 1.3851652
23220 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  2.651109 -0.629285  3.758090  2.151322  1.138241
23220 more elements ...

$df.residual.zeros
[1] 54 54 54 54 54
23220 more elements ...

$df.prior
[1] 11.2477 11.2477 11.2477 11.2477 11.2477
23220 more elements ...

$var.post
[1] 1.5497571 0.5400086 0.4713473 0.8038724 1.0121531
23220 more elements ...

$var.prior
[1] 0.9825569 0.7189235 0.7890759 1.0455749 1.0657926
23220 more elements ...

$samples
52 more rows ...

$genes
23220 more rows ...


$bone_non_sclerotic_hip_vs_tibia$mds_plot
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$w
[1] 0.8818924

$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$h
[1] 0.6859077

$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$left
[1] 2.970551

$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$top
[1] 1.886048


$bone_non_sclerotic_hip_vs_tibia$mds_plot$text
$bone_non_sclerotic_hip_vs_tibia$mds_plot$text$x
[1] 3.326605 3.326605

$bone_non_sclerotic_hip_vs_tibia$mds_plot$text$y
[1] 1.657412 1.428776



$bone_non_sclerotic_hip_vs_tibia$ql_disp_plot
NULL

$bone_non_sclerotic_hip_vs_tibia$boxplot_gg


$bone_sclerotic_hip_vs_tibia
$bone_sclerotic_hip_vs_tibia$name
[1] "tibia-vs-hip"

$bone_sclerotic_hip_vs_tibia$results
Coefficient:  grouptibia 

$bone_sclerotic_hip_vs_tibia$colsums_samples

$bone_sclerotic_hip_vs_tibia$normalized_matrix
                          X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X105_tibia_sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_sclerotic_adipocyte
TSPAN6                                      6.109276e+00                9.139053e+00                   4.490814e+00                   9.944566e+00                6.835935e+00                   4.602659e+00
TNMD                                        0.000000e+00                0.000000e+00                   1.496938e+00                   0.000000e+00                0.000000e+00                   0.000000e+00
DPM1                                        9.842723e+00                1.370858e+01                   9.480608e+00                   1.370140e+01                6.835935e+00                   5.523191e+00
SCYL3                                       8.824510e+00                3.263947e+00                   2.993876e+00                   2.872875e+00                6.214486e+00                   4.602659e+00
C1orf112                                    0.000000e+00                0.000000e+00                   0.000000e+00                   4.861788e+00                0.000000e+00                   0.000000e+00
FGR                                         3.937089e+01                2.033439e+02                   6.536630e+01                   8.066148e+01                6.960224e+01                   3.221861e+01
CFH                                         1.357617e+00                3.590342e+00                   6.486732e+00                   5.082778e+00                2.485794e+00                   0.000000e+00
FUCA2                                       2.647353e+01                1.893090e+01                   1.297346e+01                   1.723725e+01                1.719341e+01                   1.564904e+01
GCLC                                        2.579472e+01                1.958368e+01                   8.981628e+00                   3.469548e+01                1.035748e+01                   3.590074e+01
NFYA                                        1.764902e+01                3.492424e+01                   5.239283e+01                   1.790022e+01                3.148673e+01                   5.339084e+01
STPG1                                       1.086094e+01                6.201500e+00                   5.488773e+00                   6.187730e+00                8.285982e-01                   2.761595e+00
NIPAL3                                      8.824510e+00                1.044463e+01                   1.297346e+01                   7.955653e+00                1.222182e+01                   8.284786e+00
LAS1L                                       3.088579e+01                3.753540e+01                   4.141529e+01                   4.751293e+01                2.216500e+01                   3.221861e+01
ENPP4                                       0.000000e+00                4.569526e+00                   4.989794e-01                   1.767923e+00                3.314393e+00                   3.682127e+00
SEMA3F                                      4.072851e+01                2.252124e+01                   3.293264e+01                   2.497191e+01                5.178738e+01                   2.025170e+01
ANKIB1                                      1.357617e+01                1.370858e+01                   1.447040e+01                   9.723575e+00                1.056463e+01                   3.129808e+01
CYP51A1                                     1.663081e+01                8.159869e+00                   1.147653e+01                   1.679527e+01                8.700281e+00                   1.196691e+01
                          X128_tibia_sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_sclerotic_adipocyte
TSPAN6                                   3.431038e+00                   2.926414e+00                1.351337e+01                   7.165749e+00                6.338898e+00                   9.943108e+00
TNMD                                     0.000000e+00                   0.000000e+00                0.000000e+00                   0.000000e+00                2.016922e+00                   0.000000e+00
DPM1                                     1.315231e+01                   1.268113e+01                2.852823e+01                   1.213554e+01                1.296593e+01                   2.272710e+01
SCYL3                                    3.431038e+00                   0.000000e+00                1.051040e+01                   3.582875e+00                5.474503e+00                   2.840888e+00
C1orf112                                 0.000000e+00                   0.000000e+00                0.000000e+00                   1.618072e+00                1.152527e+00                   0.000000e+00
FGR                                      8.177308e+01                   1.950942e+02                8.558469e+01                   1.089887e+02                4.811800e+01                   4.460194e+02
CFH                                      4.002878e+00                   3.901885e+00                6.005943e+00                   2.542685e+00                4.610108e+00                   0.000000e+00
FUCA2                                    2.001439e+01                   1.170565e+01                3.002972e+00                   1.583399e+01                4.898240e+00                   4.261332e+00
GCLC                                     5.146558e+00                   2.536225e+01                2.852823e+01                   2.958761e+01                7.203294e+00                   1.193173e+02
NFYA                                     3.831326e+01                   1.658301e+01                2.702674e+01                   2.646704e+01                2.650812e+01                   5.681776e+01
STPG1                                    1.543967e+01                   0.000000e+00                1.351337e+01                   1.849226e+00                1.728790e+00                   8.522664e+00
NIPAL3                                   2.802015e+01                   3.901885e+00                1.801783e+01                   6.472290e+00                2.103362e+01                   5.681776e+00
LAS1L                                    2.287359e+01                   1.073018e+01                3.903863e+01                   3.409510e+01                4.033844e+01                   2.130666e+01
ENPP4                                    3.431038e+00                   3.901885e+00                4.504457e+00                   3.351721e+00                3.457581e+00                   4.261332e+00
SEMA3F                                   3.145119e+01                   1.463207e+01                1.951931e+01                   1.421592e+01                3.515207e+01                   1.704533e+01
ANKIB1                                   9.721275e+00                   1.560754e+01                1.201189e+01                   1.502496e+01                2.362680e+01                   0.000000e+00
CYP51A1                                  1.029312e+01                   2.926414e+00                0.000000e+00                   1.109535e+01                9.508348e+00                   1.420444e+00
                          X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_sclerotic_adipocyte X155_Tibia_sclerotic_pellet
TSPAN6                                      1.153695e+01                    9.347641                   0.000000e+00                4.696195e+01                   7.279063e+00                3.728945e+00
TNMD                                        0.000000e+00                    0.000000                   0.000000e+00                0.000000e+00                   0.000000e+00                0.000000e+00
DPM1                                        9.439323e+00                    0.000000                   2.626272e+01                4.696195e+00                   1.273836e+01                1.193262e+01
SCYL3                                       7.341696e+00                    1.335377                   0.000000e+00                6.261594e+00                   4.549414e-01                7.457889e-01
C1orf112                                    6.992091e-01                    0.000000                   0.000000e+00                0.000000e+00                   0.000000e+00                0.000000e+00
FGR                                         5.348950e+01                   85.464149                   1.505729e+02                3.130797e+01                   5.277321e+01                8.576573e+01
CFH                                         4.544859e+00                   26.707546                   8.754239e+00                1.565398e+01                   5.914239e+00                1.044105e+01
FUCA2                                       1.608181e+01                   10.683019                   1.400678e+01                0.000000e+00                   2.593166e+01                5.220523e+00
GCLC                                        1.713062e+01                   30.713678                   2.276102e+01                1.252319e+01                   9.553770e+00                1.416999e+01
NFYA                                        3.705808e+01                   30.713678                   0.000000e+00                3.287337e+01                   2.866131e+01                1.118683e+01
STPG1                                       8.040905e+00                    5.341509                   0.000000e+00                6.261594e+00                   2.729649e+00                2.237367e+00
NIPAL3                                      1.258576e+01                   29.378301                   1.750848e+01                2.504637e+01                   7.279063e+00                2.983156e+01
LAS1L                                       2.726916e+01                   41.396697                   1.750848e+01                4.070036e+01                   4.594909e+01                2.461104e+01
ENPP4                                       4.894464e+00                    0.000000                   0.000000e+00                4.696195e+00                   6.369180e+00                1.491578e+00
SEMA3F                                      3.426125e+01                   28.042924                   2.451187e+01                1.721938e+01                   1.410318e+01                3.505208e+01
ANKIB1                                      1.433379e+01                   18.695283                   1.400678e+01                1.408859e+01                   7.734005e+00                9.695256e+00
CYP51A1                                     1.188656e+01                   38.725942                   4.377120e+01                0.000000e+00                   1.637789e+01                1.118683e+01
                          X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_sclerotic_adipocyte X160_Tibia_sclerotic_pellet
TSPAN6                                      2.534194e+00                1.450756e+01                   8.972121e+00                6.528036e+00                   8.784107e+00                3.183674e+00
TNMD                                        0.000000e+00                0.000000e+00                   1.451373e+00                0.000000e+00                   3.331903e+00                0.000000e+00
DPM1                                        9.412721e+00                1.994789e+01                   1.121515e+01                9.671165e+00                   1.262084e+01                9.647496e+00
SCYL3                                       1.810139e+00                9.067223e-01                   3.958289e-01                3.626687e+00                   3.331903e+00                3.858998e+00
C1orf112                                    0.000000e+00                9.067223e-01                   2.638859e-01                2.417791e-01                   8.077339e-01                5.788497e-01
FGR                                         2.642802e+01                7.616467e+01                   2.889551e+01                3.457441e+01                   2.100108e+01                4.341373e+01
CFH                                         1.086083e+00                9.067223e-01                   2.111087e+00                2.901349e+00                   3.836736e+00                5.113173e+00
FUCA2                                       7.602582e+00                9.067223e+00                   1.926367e+01                2.877171e+01                   1.554888e+01                9.743971e+00
GCLC                                        2.679005e+01                1.722772e+01                   4.301341e+01                1.885877e+01                   3.382386e+01                2.672356e+01
NFYA                                        2.570397e+01                1.813445e+01                   3.179825e+01                3.167306e+01                   3.483353e+01                2.527644e+01
STPG1                                       1.448111e+00                6.347056e+00                   5.937433e+00                9.671165e-01                   8.279273e+00                2.411874e+00
NIPAL3                                      8.688666e+00                4.533611e+00                   1.095127e+01                8.462269e+00                   1.039957e+01                1.061225e+01
LAS1L                                       5.104591e+01                5.258989e+01                   4.182592e+01                2.466147e+01                   4.230507e+01                3.444156e+01
ENPP4                                       3.620277e+00                9.067223e-01                   4.090232e+00                4.110245e+00                   3.029002e+00                1.833024e+00
SEMA3F                                      3.258250e+01                1.994789e+01                   1.886784e+01                4.956472e+01                   2.736199e+01                7.139147e+01
ANKIB1                                      1.556719e+01                9.067223e+00                   1.768036e+01                1.063828e+01                   1.615468e+01                1.157699e+01
CYP51A1                                     1.520516e+01                1.722772e+01                   2.731219e+01                1.910055e+01                   1.726531e+01                1.292764e+01
                          X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_sclerotic_adipocyte
TSPAN6                                      6.647082e+00                1.557189e+01                   1.989227e+00                5.762564e+00               7.098767e+00                 4.784526e+00
TNMD                                        0.000000e+00                0.000000e+00                   0.000000e+00                0.000000e+00               0.000000e+00                 1.196132e+00
DPM1                                        8.459923e+00                9.966012e+00                   3.315378e+00                9.220102e+00               3.042329e+01                 1.510116e+01
SCYL3                                       2.296265e+00                2.491503e+00                   3.978454e+00                4.840553e+00               1.014110e+00                 2.990329e-01
C1orf112                                    1.087704e+00                1.245752e+00                   0.000000e+00                0.000000e+00               0.000000e+00                 1.196132e+00
FGR                                         4.332689e+01                5.813507e+01                   1.336098e+02                4.310398e+01               9.329808e+01                 7.849614e+01
CFH                                         1.571129e+00                2.076253e-01                   1.326151e+00                2.996533e+00               1.014110e+01                 5.980658e+00
FUCA2                                       1.099790e+01                2.325403e+01                   3.348532e+01                2.420277e+01               0.000000e+00                 7.924372e+00
GCLC                                        2.652790e+01                1.744052e+01                   2.055535e+01                1.797920e+01               1.419753e+01                 4.036944e+01
NFYA                                        2.852203e+01                2.449978e+01                   1.491920e+01                1.106412e+01               3.447972e+01                 4.231316e+01
STPG1                                       4.229962e+00                7.474509e+00                   6.630757e+00                8.067589e+00               9.126986e+00                 1.046615e+01
NIPAL3                                      1.281074e+01                1.889390e+01                   1.525074e+01                1.498267e+01               1.521164e+01                 2.033424e+01
LAS1L                                       2.580277e+01                2.719891e+01                   4.376300e+01                3.319237e+01               2.028219e+01                 5.143366e+01
ENPP4                                       4.109106e+00                4.983006e+00                   2.652303e+00                2.074523e+00               2.028219e+00                 2.541780e+00
SEMA3F                                      3.251028e+01                3.965642e+01                   2.685457e+01                3.895493e+01               2.332452e+01                 4.620058e+01
ANKIB1                                      1.559043e+01                1.453377e+01                   1.624535e+01                8.298092e+00               6.084657e+00                 2.182940e+01
CYP51A1                                     1.335459e+01                1.598714e+01                   1.027767e+01                2.374176e+01               1.825397e+01                 1.480213e+01
                          X108_Hip_sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet
TSPAN6                                 3.625694e+00                 1.124589e+00              8.251374e-01                 6.962937e+00              0.000000e+00                 2.702499e+00              2.277740e-01
TNMD                                   0.000000e+00                 9.371572e-02              0.000000e+00                 3.481468e-01              0.000000e+00                 3.378123e-01              0.000000e+00
DPM1                                   2.406142e+01                 4.779502e+00              1.746541e+01                 6.614790e+00              5.863920e+00                 7.094059e+00              1.488123e+01
SCYL3                                  3.296085e-01                 1.874314e+00              5.225870e+00                 3.829615e+00              5.863920e+00                 1.351249e+00              3.568459e+00
C1orf112                               0.000000e+00                 1.499451e+00              4.400733e+00                 0.000000e+00              7.818561e+00                 1.013437e+00              1.366644e+00
FGR                                    2.472064e+02                 5.429889e+02              4.620770e+02                 3.481468e+01              6.938973e+01                 3.979429e+02              3.439387e+02
CFH                                    3.296085e-01                 1.968030e+00              1.100183e+00                 0.000000e+00              2.931960e+00                 0.000000e+00              2.277740e-01
FUCA2                                  1.318434e+01                 1.883686e+01              8.526420e+00                 1.984437e+01              1.221650e+01                 1.705952e+01              1.313496e+01
GCLC                                   2.274299e+01                 5.501113e+01              6.614852e+01                 1.288143e+01              1.417114e+01                 5.658357e+01              3.560866e+01
NFYA                                   4.812285e+01                 4.779502e+01              4.717036e+01                 4.247392e+01              2.492166e+01                 3.614592e+01              5.375465e+01
STPG1                                  3.955302e+00                 4.592070e+00              6.188531e+00                 2.785175e+00              4.886600e-01                 0.000000e+00              2.049966e+00
NIPAL3                                 2.109495e+01                 1.246419e+01              1.347724e+01                 9.748112e+00              1.661444e+01                 1.283687e+01              3.401424e+01
LAS1L                                  5.735188e+01                 4.385896e+01              4.428237e+01                 4.874056e+01              4.251342e+01                 5.303654e+01              4.851585e+01
ENPP4                                  1.087708e+01                 1.499451e+00              4.400733e+00                 2.785175e+00              9.773201e-01                 2.026874e+00              6.377671e+00
SEMA3F                                 3.955302e+01                 1.499451e+01              1.388981e+01                 6.614790e+00              5.179796e+01                 1.486374e+01              7.592465e+00
ANKIB1                                 1.483238e+01                 2.155462e+01              1.499000e+01                 2.506657e+01              3.176290e+01                 2.094437e+01              1.457753e+01
CYP51A1                                1.120669e+01                 1.049616e+01              5.363393e+00                 1.775549e+01              6.841241e+00                 7.431872e+00              7.212842e+00
                          X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_sclerotic_adipocyte
TSPAN6                                    2.041447e+00              6.260208e-01                 2.640983e+00              0.000000e+00                 3.508769e+00              2.178249e+00                 8.616814e+00
TNMD                                      2.551809e-01              0.000000e+00                 0.000000e+00              0.000000e+00                 0.000000e+00              0.000000e+00                 0.000000e+00
DPM1                                      2.066966e+01              3.756125e+00                 1.419529e+01              1.138498e+00                 1.197109e+01              1.176255e+01                 1.126814e+01
SCYL3                                     2.041447e+00              1.085103e+01                 3.301229e-01              9.107981e+00                 3.439970e+00              2.323466e+00                 3.579292e+00
C1orf112                                  2.296628e+00              2.086736e-01                 1.980737e+00              0.000000e+00                 2.751976e+00              3.775632e+00                 7.953982e-01
FGR                                       6.175379e+01              4.569952e+01                 1.914713e+01              2.903169e+01                 2.251116e+02              3.499720e+02                 2.704354e+01
CFH                                       1.531086e+00              7.094902e+00                 8.253073e+00              3.984742e+00                 1.513587e+00              0.000000e+00                 2.253628e+00
FUCA2                                     1.454531e+01              1.356378e+01                 2.013750e+01              2.504695e+01                 1.231509e+01              1.786164e+01                 1.458230e+01
GCLC                                      2.245592e+01              3.130104e+01                 1.551578e+01              1.935446e+01                 7.939450e+01              7.231787e+01                 2.717611e+01
NFYA                                      4.210485e+01              2.524950e+01                 3.961475e+01              2.675469e+01                 5.669070e+01              6.055533e+01                 2.704354e+01
STPG1                                     2.296628e+00              1.460715e+00                 1.188442e+01              2.846244e+00                 3.577568e+00              2.033033e+00                 2.651327e+00
NIPAL3                                    1.352459e+01              1.961532e+01                 8.913319e+00              2.220070e+01                 2.015822e+01              2.468682e+01                 9.279646e+00
LAS1L                                     2.985617e+01              3.463982e+01                 4.951844e+01              2.447770e+01                 4.258682e+01              3.339982e+01                 3.513009e+01
ENPP4                                     1.020724e+00              0.000000e+00                 6.602458e-01              0.000000e+00                 4.196763e+00              3.049549e+00                 6.628319e+00
SEMA3F                                    1.862821e+01              2.566685e+01                 2.244836e+01              4.895540e+01                 2.132781e+01              8.422563e+00                 1.816159e+01
ANKIB1                                    1.633158e+01              2.191073e+01                 3.268217e+01              1.650822e+01                 2.800135e+01              1.945903e+01                 2.651327e+01
CYP51A1                                   9.696876e+00              1.418980e+01                 9.243441e+00              1.081573e+01                 8.118328e+00              8.132130e+00                 8.219115e+00
                          X150_Hip_sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet
TSPAN6                                 2.307693e+00                 1.364561e+00              7.489405e-01                 2.983063e+00              9.696885e-01                 0.000000e+00              0.000000e+00
TNMD                                   0.000000e+00                 0.000000e+00              0.000000e+00                 0.000000e+00              3.232295e-01                 0.000000e+00              0.000000e+00
DPM1                                   9.230770e+00                 7.060122e+00              8.737639e+00                 1.161825e+01              1.147465e+01                 5.557702e+00              8.567166e+00
SCYL3                                  1.153846e+01                 5.280259e+00              5.492230e+00                 4.239090e+00              4.040369e+00                 4.631419e+00              0.000000e+00
C1orf112                               7.692309e-01                 3.263081e+00              4.743290e+00                 2.904562e+00              1.454533e+00                 1.389426e+00              0.000000e+00
FGR                                    2.692308e+01                 3.851623e+02              2.436553e+02                 9.844109e+01              3.372900e+02                 1.227326e+02              1.670597e+02
CFH                                    2.307693e+01                 5.339588e-01              1.747528e+00                 3.532575e+00              2.262607e+00                 0.000000e+00              1.070896e+01
FUCA2                                  2.307693e+01                 1.993446e+01              1.173340e+01                 1.334528e+01              1.098980e+01                 9.725979e+00              9.638062e+00
GCLC                                   2.538462e+01                 1.282688e+02              5.317477e+01                 4.717950e+01              6.828224e+01                 6.483986e+01              1.392164e+01
NFYA                                   6.230770e+01                 5.968473e+01              4.343855e+01                 3.838732e+01              4.129257e+01                 4.862989e+01              2.998508e+01
STPG1                                  6.153847e+00                 4.983615e+00              1.497881e+00                 4.474595e+00              3.959562e+00                 4.631419e-01              0.000000e+00
NIPAL3                                 2.538462e+01                 3.441068e+01              3.470091e+01                 1.860490e+01              2.311091e+01                 3.010422e+01              5.247389e+01
LAS1L                                  4.384616e+01                 6.615156e+01              4.318890e+01                 5.196810e+01              6.779739e+01                 4.214591e+01              6.318285e+01
ENPP4                                  3.076923e+00                 6.229519e+00              4.992936e+00                 4.710100e+00              1.212111e+00                 0.000000e+00              0.000000e+00
SEMA3F                                 2.769231e+01                 4.864958e+00              7.239758e+00                 2.488503e+01              4.040369e+00                 1.065226e+01              2.677239e+01
ANKIB1                                 3.000000e+01                 2.343486e+01              1.123411e+01                 2.143096e+01              2.060588e+01                 1.482054e+01              2.141791e+00
CYP51A1                                1.076923e+01                 5.932875e+00              1.223269e+01                 8.870688e+00              9.292849e+00                 1.852567e+00              8.567166e+00
                          X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                                    1.565662e+00              0.000000e+00                 1.129774e+01              7.711789e+00             8.733780e+00
TNMD                                      2.012994e+00              0.000000e+00                 0.000000e+00              0.000000e+00             0.000000e+00
DPM1                                      1.252530e+01              8.845968e+00                 1.435118e+01              8.945676e+00             2.074273e+01
SCYL3                                     6.933647e+00              3.159274e+00                 8.549639e+00              4.627074e+00             1.091723e+00
C1orf112                                  6.709981e-01              8.424731e-01                 2.290082e+00              9.254147e-01             1.910514e+00
FGR                                       1.538822e+02              3.609997e+02                 3.496191e+01              1.218463e+02             4.148546e+01
CFH                                       0.000000e+00              1.684946e+00                 2.595426e+00              8.328732e+00             8.187919e+00
FUCA2                                     1.252530e+01              1.663884e+01                 1.480920e+01              1.357275e+01             2.592841e+01
GCLC                                      5.233785e+01              3.327769e+01                 3.877872e+01              2.591161e+01             1.637584e+01
NFYA                                      4.518054e+01              4.802097e+01                 3.938941e+01              3.393187e+01             1.937807e+01
STPG1                                     3.802322e+00              2.738038e+00                 1.282446e+01              3.393187e+00             2.183445e+00
NIPAL3                                    1.118330e+01              1.706008e+01                 1.007636e+01              5.552488e+00             2.974944e+01
LAS1L                                     3.914155e+01              3.559449e+01                 4.519095e+01              3.763353e+01             3.493512e+01
ENPP4                                     8.051977e+00              3.159274e+00                 3.053442e-01              2.159301e+00             8.187919e-01
SEMA3F                                    2.348493e+01              1.832379e+01                 3.480924e+01              3.177257e+01             2.456376e+01
ANKIB1                                    2.460326e+01              8.635350e+00                 3.908406e+01              2.128454e+01             1.528412e+01
CYP51A1                                   5.144319e+00              1.284772e+01                 2.213746e+01              8.328732e+00             6.004474e+00
 [ reached getOption("max.print") -- omitted 23174 rows ]

$bone_sclerotic_hip_vs_tibia$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) batchpellet  grouptibia
TSPAN6     -12.72109 -0.03627021  1.04015184
TNMD       -15.05383 -1.31704314  0.69421662
DPM1       -11.43371  0.05389351  0.09336044
SCYL3      -12.51405  0.24892662 -0.18079516
C1orf112   -13.04351 -0.22212393 -1.25611269
23186 more rows ...

$fitted.values
         X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X105_tibia_sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet
TSPAN6                        24.854438                  24.8810264                      16.905913                      38.172262                   39.203738                      9.1639435                  14.2015950
TNMD                           1.730266                   0.3899298                       1.176922                       2.657400                    0.614392                      0.6379570                   0.2225642
DPM1                          34.936814                  38.3459782                      23.763914                      53.657107                   60.419762                     12.8813612                  21.8871217
SCYL3                          8.963097                  11.9736155                       6.096671                      13.765819                   18.866203                      3.3047344                   6.8343016
C1orf112                       1.747284                   1.4375199                       1.188497                       2.683535                    2.265025                      0.6442313                   0.8205078
         X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet
TSPAN6                        8.6478223                  5.40866684                      72.987971                  28.1851492                      5.9387779                      24.129265                  6.08145438
TNMD                          0.6020267                  0.08476339                       5.081130                   0.4417112                      0.4134339                       1.679783                  0.09530716
DPM1                         12.1558719                  8.33569394                     102.596051                  43.4382047                      8.3478846                      33.917470                  9.37257625
SCYL3                         3.1186089                  2.60283864                      26.321186                  13.5636743                      2.1416635                       8.701583                  2.92660741
C1orf112                      0.6079477                  0.31248977                       5.131103                   1.6284181                      0.4175000                       1.696303                  0.35136057
         X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_sclerotic_adipocyte X155_Tibia_sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_sclerotic_adipocyte
TSPAN6                        4.8180666                  5.18783980                      18.542389                  10.8891884                      23.301257                   8.9564761                      63.934456
TNMD                          0.3354145                  0.08130264                       1.290847                   0.1706529                       1.622140                   0.1403638                       4.450860
DPM1                          6.7725490                  7.99536115                      26.064239                  16.7821284                      32.753576                  13.8034835                      89.869915
SCYL3                         1.7375086                  2.49656898                       6.686823                   5.2402563                       8.402984                   4.3101679                      23.056274
C1orf112                      0.3387133                  0.29973132                       1.303542                   0.6291310                       1.638094                   0.5174671                       4.494635
         X159_Tibia_sclerotic_pellet X160_Tibia_sclerotic_adipocyte X160_Tibia_sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_sclerotic_pellet
TSPAN6                    33.5886594                      83.549307                   84.177661                     139.599164                  39.1139136                      25.444158                  35.2318722
TNMD                       0.5263938                       5.816368                    1.319213                       9.718334                   0.6129843                       1.771320                   0.5521458
DPM1                      51.7659513                     117.441668                  129.732380                     196.228541                  60.2813266                      35.765759                  54.2984273
SCYL3                     16.1640314                      30.129853                   40.509219                      50.342755                  18.8229759                       9.175764                  16.9548025
C1orf112                   1.9406099                       5.873572                    4.863427                       9.813914                   2.2598356                       1.788741                   2.0355478
         X99_Tibia_sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6                    8.0080466                    19.822691                 8.6565215                    31.625629                20.7475502                    8.5131274                 5.8389536
TNMD                      0.1255003                     1.705185                 0.1676337                     2.720496                 0.4017768                    0.7323153                 0.1130715
DPM1                     12.3417891                    72.226589                34.5819973                   115.232147                82.8845312                   31.0187023                23.3260761
SCYL3                     3.8537506                    24.405990                14.2226357                    38.937941                34.0881552                   10.4814883                 9.5933812
C1orf112                  0.4626709                    14.388414                 5.1639239                    22.955643                12.3766539                    6.1793021                 3.4831442
         X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6                      17.547129                37.5801968                   11.6145763                13.6733324                    8.9779243                 5.0123307                    43.079138
TNMD                         1.509437                 0.7277414                    0.9991077                 0.2647844                    0.7722979                 0.0970639                     3.705749
DPM1                        63.935279               150.1293867                   42.3192403                54.6236899                   32.7122508                20.0237945                   156.964520
SCYL3                       21.604285                61.7441367                   14.3000380                22.4652392                   11.0537530                 8.2352425                    53.039671
C1orf112                    12.736684                22.4179281                    8.4305065                 8.1566306                    6.5166776                 2.9900341                    31.269238
         X146_Hip_sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet
TSPAN6                  19.6483260                    22.357242                3.70924191                    49.955852                11.4291995                    37.754848                35.3094403
TNMD                     0.3804903                     1.923212                0.07182956                     4.297296                 0.2213267                     3.247743                 0.6837681
DPM1                    78.4932329                    81.461559               14.81807604                   182.020734                45.6585878                   137.564765               141.0579259
SCYL3                   32.2821335                    27.526567                6.09427197                    61.506383                18.7781363                    46.484326                58.0132915
C1orf112                11.7209275                    16.228132                2.21269514                    36.260740                 6.8179253                    27.404572                21.0633409
         X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                      6.3993752                 2.6643708                    13.251089                13.5470825                     19.41297                 9.2496799               10.4541706
TNMD                        0.5504863                 0.0515956                     1.139884                 0.2623396                      1.66994                 0.1791203                0.2024453
DPM1                       23.3169673                10.6439131                    48.282091                54.1193332                     70.73370                36.9516099               41.7634379
SCYL3                       7.8790053                 4.3775522                    16.314937                22.2578110                     23.90153                15.1971929               17.1761670
C1orf112                    4.6450230                 1.5893922                     9.618379                 8.0813181                     14.09101                 5.5177641                6.2362857
23186 more rows ...

$deviance
[1] 71.42430 29.81002 38.80787 39.25253 37.47377
23186 more elements ...

$iter
[1] 7 6 3 3 6
23186 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
23186 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X105_tibia_sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet
TSPAN6                               18                          28                              9                             45                          33                              5                           6
TNMD                                  0                           0                              3                              0                           0                              0                           0
DPM1                                 29                          42                             19                             62                          33                              6                          23
SCYL3                                26                          10                              6                             13                          30                              5                           6
C1orf112                              0                           0                              0                             22                           0                              0                           0
         X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet
TSPAN6                                3                           9                             62                          22                              7                             33                           7
TNMD                                  0                           0                              0                           7                              0                              0                           0
DPM1                                 13                          19                            105                          45                             16                             27                           0
SCYL3                                 0                           7                             31                          19                              2                             21                           1
C1orf112                              0                           0                             14                           4                              0                              2                           0
         X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_sclerotic_adipocyte X155_Tibia_sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_sclerotic_adipocyte
TSPAN6                                0                          30                             16                           5                              7                          16                             68
TNMD                                  0                           0                              0                           0                              0                           0                             11
DPM1                                 15                           3                             28                          16                             26                          22                             85
SCYL3                                 0                           4                              1                           1                              5                           1                              3
C1orf112                              0                           0                              0                           0                              0                           1                              2
         X159_Tibia_sclerotic_pellet X160_Tibia_sclerotic_adipocyte X160_Tibia_sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_sclerotic_pellet
TSPAN6                            27                             87                          33                            110                          75                              6                          25
TNMD                               0                             33                           0                              0                           0                              0                           0
DPM1                              40                            125                         100                            140                          48                             10                          40
SCYL3                             15                             33                          40                             38                          12                             12                          21
C1orf112                           1                              8                           6                             18                           6                              0                           0
         X99_Tibia_sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6                            7                           32                        11                           12                         6                           20                         0
TNMD                              0                            8                         0                            1                         0                            1                         0
DPM1                             30                          101                        73                           51                       127                           19                        12
SCYL3                             1                            2                         1                           20                        38                           11                        12
C1orf112                          0                            8                         0                           16                        32                            0                        16
         X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6                             16                         3                            8                         3                            8                         0                           51
TNMD                                2                         0                            1                         0                            0                         0                            0
DPM1                               42                       196                           81                        18                           43                         2                          174
SCYL3                               8                        47                            8                        52                            1                        16                           50
C1orf112                            6                        18                            9                         1                            6                         0                           40
         X146_Hip_sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet
TSPAN6                          15                           65                         3                           23                         3                           38                        12
TNMD                             0                            0                         0                            0                         0                            0                         4
DPM1                            81                           85                        12                          119                        35                          148                       142
SCYL3                           16                           27                        15                           89                        22                           54                        50
C1orf112                        26                            6                         1                           55                        19                           37                        18
         X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                              0                         0                            7                         0                           74                        25                       32
TNMD                                0                         0                            9                         0                            0                         0                        0
DPM1                               12                         8                           56                        42                           94                        29                       76
SCYL3                              10                         0                           31                        15                           56                        15                        4
C1orf112                            3                         0                            3                         4                           15                         3                        7
23186 more rows ...

$unshrunk.coefficients
         (Intercept) batchpellet  grouptibia
TSPAN6     -12.72903 -0.03801510  1.04599440
TNMD       -15.18219 -1.52914827  0.83438695
DPM1       -11.43605  0.05402422  0.09351826
SCYL3      -12.52103  0.25050538 -0.18192739
C1orf112   -13.04944 -0.23422729 -1.28857555
23186 more rows ...

$df.residual
[1] 53 53 53 53 53
23186 more elements ...

$design
                               (Intercept) batchpellet grouptibia
X102_tibia_sclerotic_adipocyte           1           0          1
X102_tibia_sclerotic_pellet              1           1          1
X105_tibia_sclerotic_adipocyte           1           0          1
X109_tibia_sclerotic_adipocyte           1           0          1
X109_tibia_sclerotic_pellet              1           1          1
51 more rows ...

$offset
         [,1]     [,2]    [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]   [,14]    [,15]    [,16]   [,17]    [,18]    [,19]    [,20]   [,21]    [,22]    [,23]    [,24]
[1,] 14.89607 14.93516 14.5107 15.32515 15.38982 13.89831 14.37441 13.84035 13.40906 15.97333 15.05985 13.46454 14.86646 13.5263 13.25541 13.36737 14.6031 14.10882 14.83155 13.91343 15.8409 15.23524 16.10847 16.15398
        [,25]    [,26]    [,27]  [,28]   [,29]    [,30]    [,31]  [,32]    [,33]    [,34]   [,35]    [,36]    [,37]    [,38]    [,39]   [,40]    [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]   [,49]
[1,] 16.62181 15.38753 14.91952 15.283 13.8015 15.71586 14.92536 16.183 15.79948 14.87064 14.5316 15.59392 16.39352 15.18129 15.38249 14.9238 14.37895 16.49207 15.74504 15.83618 14.07787 16.64017 15.20322 16.36015 16.3312
        [,50]    [,51]    [,52]    [,53]    [,54]    [,55]    [,56]
[1,] 14.58523 13.74702 15.31311 15.37322 15.69497 14.99164 15.11405
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 56
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23186 more rows ...

$dispersion
[1] 0.6676478 6.3532610 0.4097687 0.8868782 2.2707671
23186 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  2.5764710 -0.5620076  3.5953853  2.0772338  0.7359507
23186 more elements ...

$df.residual.zeros
[1] 53 53 53 53 53
23186 more elements ...

$df.prior
[1] 17.87419 17.87419 17.87419 17.87419 17.87419
23186 more elements ...

$var.post
[1] 1.2728244 0.5708394 0.7734800 0.8288521 0.7752235
23186 more elements ...

$var.prior
[1] 1.0510181 0.5957056 0.8958111 1.0904938 0.9773630
23186 more elements ...

$samples
51 more rows ...

$genes
23186 more rows ...


$bone_sclerotic_hip_vs_tibia$mds_plot
$bone_sclerotic_hip_vs_tibia$mds_plot$rect
$bone_sclerotic_hip_vs_tibia$mds_plot$rect$w
[1] 0.8358968

$bone_sclerotic_hip_vs_tibia$mds_plot$rect$h
[1] 0.7806285

$bone_sclerotic_hip_vs_tibia$mds_plot$rect$left
[1] 3.299757

$bone_sclerotic_hip_vs_tibia$mds_plot$rect$top
[1] 2.167356


$bone_sclerotic_hip_vs_tibia$mds_plot$text
$bone_sclerotic_hip_vs_tibia$mds_plot$text$x
[1] 3.637241 3.637241

$bone_sclerotic_hip_vs_tibia$mds_plot$text$y
[1] 1.907147 1.646937



$bone_sclerotic_hip_vs_tibia$ql_disp_plot
NULL

$bone_sclerotic_hip_vs_tibia$boxplot_gg


$hip_adipocytes_sclerotic_vs_non_sclerotic
$hip_adipocytes_sclerotic_vs_non_sclerotic$name
[1] "HSA-vs-HNSA"

$hip_adipocytes_sclerotic_vs_non_sclerotic$results
Coefficient:  groupHSA 

$hip_adipocytes_sclerotic_vs_non_sclerotic$colsums_samples

$hip_adipocytes_sclerotic_vs_non_sclerotic$normalized_matrix
                          X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte
TSPAN6                                        5.915820e+00                 4.898332e+00                     4.952515e+00                 1.214547e+00                     0.000000e+00                 7.319304e+00
TNMD                                          9.859699e-01                 1.224583e+00                     0.000000e+00                 1.012123e-01                     4.238497e-01                 3.659652e-01
DPM1                                          1.321200e+01                 1.546036e+01                     1.287654e+01                 5.161827e+00                     1.102009e+01                 6.953338e+00
SCYL3                                         5.915820e+00                 3.061457e-01                     1.839506e+00                 2.024246e+00                     4.662346e+00                 4.025617e+00
C1orf112                                      1.183164e+00                 1.224583e+00                     3.537511e+00                 1.619397e+00                     0.000000e+00                 0.000000e+00
FGR                                           9.090643e+01                 8.036326e+01                     1.422079e+02                 5.864240e+02                     9.621387e+01                 3.659652e+01
CFH                                           5.915820e+00                 6.122915e+00                     1.415004e+00                 2.125458e+00                     1.907323e+00                 0.000000e+00
FUCA2                                         1.557833e+01                 8.112862e+00                     1.613105e+01                 2.034367e+01                     2.225211e+01                 2.086002e+01
GCLC                                          3.865002e+01                 4.132967e+01                     6.056219e+01                 5.941161e+01                     2.309981e+01                 1.354071e+01
NFYA                                          3.214262e+01                 4.331962e+01                     3.806362e+01                 5.161827e+01                     4.068957e+01                 4.464775e+01
STPG1                                         1.163445e+01                 1.071510e+01                     3.820512e+00                 4.959402e+00                     2.331173e+00                 2.927721e+00
NIPAL3                                        7.690566e+00                 2.081791e+01                     1.839506e+01                 1.346123e+01                     1.271549e+01                 1.024703e+01
LAS1L                                         6.231330e+01                 5.265707e+01                     6.296770e+01                 4.736735e+01                     4.111342e+01                 5.123513e+01
ENPP4                                         3.155104e+00                 2.602239e+00                     8.490026e-01                 1.619397e+00                     5.933895e+00                 2.927721e+00
SEMA3F                                        5.521432e+01                 4.729952e+01                     2.603608e+01                 1.619397e+01                     1.144394e+01                 6.953338e+00
ANKIB1                                        2.760716e+01                 2.234864e+01                     2.957359e+01                 2.327883e+01                     2.352366e+01                 2.634949e+01
CYP51A1                                       1.005689e+01                 1.515421e+01                     1.160304e+01                 1.133578e+01                     6.993519e+00                 1.866422e+01
KRIT1                                         1.045128e+01                 8.878226e+00                     9.056028e+00                 1.639639e+01                     1.059624e+01                 1.756633e+01
RAD52                                         7.296178e+00                 1.071510e+01                     1.415004e+01                 5.667888e+00                     8.053143e+00                 1.390668e+01
MYH16                                         0.000000e+00                 0.000000e+00                     0.000000e+00                 0.000000e+00                     4.238497e-01                 0.000000e+00
BAD                                           3.470614e+01                 2.816541e+01                     2.518708e+01                 3.906794e+01                     3.751069e+01                 6.148215e+01
LAP3                                          5.639748e+01                 5.235092e+01                     5.362867e+01                 6.052495e+01                     9.324692e+01                 6.550777e+01
CD99                                          2.354496e+02                 2.015970e+02                     1.995156e+02                 1.851173e+02                     2.602437e+02                 2.898444e+02
HS3ST1                                        7.887760e+00                 9.490518e+00                     7.075022e+00                 1.143699e+01                     2.161633e+01                 2.561756e+01
AOC1                                          0.000000e+00                 0.000000e+00                     0.000000e+00                 5.060614e+00                     6.357745e-01                 0.000000e+00
WNT16                                         0.000000e+00                 1.683802e+00                     0.000000e+00                 4.048491e-01                     0.000000e+00                 0.000000e+00
HECW1                                         1.143725e+01                 9.796664e+00                     1.415004e-01                 1.214547e+00                     1.483474e+00                 5.489478e+00
MAD1L1                                        6.310208e+00                 4.898332e+00                     5.943019e+00                 1.002002e+01                     5.298121e+00                 8.783164e+00
LASP1                                         1.942361e+02                 2.037400e+02                     2.269667e+02                 3.064708e+02                     3.115295e+02                 3.125343e+02
SNX11                                         7.887760e+00                 1.239890e+01                     1.372554e+01                 1.416972e+01                     2.882178e+01                 1.280878e+01
TMEM176A                                      1.557833e+01                 1.898104e+01                     2.759259e+01                 2.145700e+01                     1.036312e+02                 2.232388e+01
M6PR                                          3.786125e+01                 4.500342e+01                     4.386514e+01                 6.730617e+01                     7.586909e+01                 3.989020e+01
KLHL13                                        0.000000e+00                 0.000000e+00                     1.698005e+00                 1.012123e+00                     4.238497e-01                 1.097896e+00
CYP26B1                                       4.377707e+01                 6.474982e+01                     1.018803e+01                 1.022244e+01                     1.398704e+01                 2.525160e+01
ICA1                                          1.163445e+01                 1.683802e+00                     7.782524e+00                 7.995771e+00                     7.205444e+00                 9.515095e+00
DBNDD1                                        1.774746e+00                 1.836874e+00                     5.660018e-01                 1.619397e+00                     0.000000e+00                 0.000000e+00
ALS2                                          1.183164e+01                 1.836874e+01                     2.858309e+01                 1.578912e+01                     1.949708e+01                 2.232388e+01
CASP10                                        1.064848e+01                 7.806716e+00                     1.556505e+01                 1.265154e+01                     2.013286e+01                 4.391582e+00
CFLAR                                         3.797956e+02                 3.805392e+02                     2.907834e+02                 5.239760e+02                     5.285405e+02                 2.404391e+02
TFPI                                          7.355336e+01                 7.240347e+01                     2.363057e+01                 1.892670e+01                     2.119248e+01                 9.515095e+00
                          X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6                                        0.000000e+00                 2.870905e+00                     6.763583e+00                 2.117607e+00                     3.357784e+00                 2.714408e+00
TNMD                                          0.000000e+00                 3.588631e-01                     0.000000e+00                 2.647009e-01                     4.477046e-01                 0.000000e+00
DPM1                                          6.165945e+00                 7.536126e+00                     1.217445e+01                 2.144077e+01                     1.253573e+01                 1.458994e+01
SCYL3                                         2.740420e+00                 1.435452e+00                     6.087225e+00                 2.117607e+00                     9.625648e+00                 3.393010e-01
C1orf112                                      4.795735e+00                 1.076589e+00                     0.000000e+00                 2.382308e+00                     4.477046e-01                 2.035806e+00
FGR                                           4.528544e+02                 4.227408e+02                     2.110238e+02                 6.405762e+01                     1.018528e+01                 1.967946e+01
CFH                                           0.000000e+00                 0.000000e+00                     0.000000e+00                 1.588205e+00                     1.455040e+00                 8.482526e+00
FUCA2                                         9.591470e+00                 1.812259e+01                     2.502526e+01                 1.508795e+01                     1.365499e+01                 2.069736e+01
GCLC                                          5.549351e+01                 6.010957e+01                     4.937416e+01                 2.329368e+01                     3.525673e+01                 1.594715e+01
NFYA                                          2.980207e+01                 3.839835e+01                     2.637797e+01                 4.367565e+01                     3.212280e+01                 4.071613e+01
STPG1                                         4.795735e+00                 0.000000e+00                     9.469017e+00                 2.382308e+00                     1.287151e+01                 1.221484e+01
NIPAL3                                        2.021060e+01                 1.363680e+01                     1.826167e+01                 1.402915e+01                     2.081826e+01                 9.161128e+00
LAS1L                                         6.268711e+01                 5.634151e+01                     3.584699e+01                 3.097001e+01                     5.383647e+01                 5.089516e+01
ENPP4                                         0.000000e+00                 2.153179e+00                     1.555624e+01                 1.058804e+00                     4.029341e+00                 6.786021e-01
SEMA3F                                        1.027658e+01                 1.578998e+01                     1.893803e+01                 1.932317e+01                     2.887694e+01                 2.307247e+01
ANKIB1                                        2.295102e+01                 2.224951e+01                     2.096711e+01                 1.694086e+01                     3.704755e+01                 3.359080e+01
CYP51A1                                       7.193603e+00                 7.894989e+00                     0.000000e+00                 1.005863e+01                     5.596307e+00                 9.500429e+00
KRIT1                                         1.130423e+01                 1.471339e+01                     6.087225e+00                 7.146925e+00                     1.231188e+01                 7.464623e+00
RAD52                                         2.432123e+01                 1.991690e+01                     1.014537e+01                 1.561735e+01                     9.961427e+00                 6.446720e+00
MYH16                                         1.027658e+00                 0.000000e+00                     0.000000e+00                 2.117607e+00                     0.000000e+00                 6.786021e-01
BAD                                           2.671910e+01                 3.498915e+01                     2.367254e+01                 4.473445e+01                     5.014291e+01                 4.444844e+01
LAP3                                          4.967011e+01                 7.446410e+01                     4.058150e+01                 3.917573e+01                     4.499431e+01                 7.532483e+01
CD99                                          8.084239e+01                 2.739920e+02                     1.170100e+02                 2.514659e+02                     2.369476e+02                 2.392072e+02
HS3ST1                                        6.508498e+00                 1.202191e+01                     4.058150e+00                 1.270564e+01                     5.596307e+00                 2.375107e+00
AOC1                                          0.000000e+00                 3.588631e-01                     1.826167e+01                 1.852906e+00                     5.596307e-01                 1.017903e+00
WNT16                                         6.851050e-01                 0.000000e+00                     0.000000e+00                 2.117607e+00                     0.000000e+00                 0.000000e+00
HECW1                                         3.768078e+00                 1.256021e+00                     0.000000e+00                 7.941027e-01                     3.022006e+00                 2.035806e+00
MAD1L1                                        7.193603e+00                 1.812259e+01                     3.381792e+00                 3.970514e+00                     5.596307e+00                 2.375107e+00
LASP1                                         3.216568e+02                 4.137692e+02                     2.117002e+02                 2.496130e+02                     2.989547e+02                 2.558330e+02
SNX11                                         1.335955e+01                 2.171122e+01                     1.961439e+01                 2.408778e+01                     1.320728e+01                 1.832226e+01
TMEM176A                                      1.781273e+01                 2.906791e+01                     2.029075e+01                 1.283799e+02                     1.298343e+01                 6.107419e+01
M6PR                                          3.357015e+01                 5.257345e+01                     2.231982e+01                 5.055787e+01                     4.074112e+01                 4.309123e+01
KLHL13                                        0.000000e+00                 1.614884e+00                     0.000000e+00                 0.000000e+00                     1.343114e+00                 0.000000e+00
CYP26B1                                       1.986805e+01                 7.715557e+00                     9.469017e+00                 4.155804e+01                     2.786961e+01                 1.832226e+01
ICA1                                          3.768078e+00                 5.024084e+00                     1.149809e+01                 7.941027e+00                     1.645314e+01                 9.500429e+00
DBNDD1                                        7.193603e+00                 0.000000e+00                     0.000000e+00                 0.000000e+00                     3.245858e+00                 3.053709e+00
ALS2                                          2.363612e+01                 1.345737e+01                     2.637797e+01                 2.541129e+01                     2.316871e+01                 1.934016e+01
CASP10                                        2.363612e+01                 7.536126e+00                     4.261057e+01                 1.614676e+01                     1.477425e+01                 1.119693e+01
CFLAR                                         4.932756e+02                 7.227503e+02                     1.907330e+02                 2.226135e+02                     2.422082e+02                 1.720256e+02
TFPI                                          8.221260e+00                 1.327794e+01                     1.014537e+01                 2.223488e+01                     1.455040e+01                 1.051833e+01
                          X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte
TSPAN6                                        3.854178e+00                 3.598384e+00                 8.695853e+00                     9.697328e-02                 1.318352e+00                     2.599099e+00
TNMD                                          4.057030e-01                 0.000000e+00                 0.000000e+00                     0.000000e+00                 0.000000e+00                     1.575211e-01
DPM1                                          1.206966e+01                 1.227684e+01                 1.137150e+01                     1.115193e+01                 6.821039e+00                     9.766310e+00
SCYL3                                         3.549901e+00                 3.527827e+00                 3.612124e+00                     2.521305e+00                 5.101449e+00                     3.859268e+00
C1orf112                                      4.158455e+00                 2.822262e+00                 8.026942e-01                     1.842492e+00                 3.152581e+00                     1.890254e+00
FGR                                           1.511244e+02                 2.308610e+02                 2.729160e+01                     3.835293e+02                 3.721192e+02                     1.381460e+02
CFH                                           1.217109e+00                 1.552244e+00                 2.274300e+00                     0.000000e+00                 5.158769e-01                     1.417690e+00
FUCA2                                         2.261794e+01                 1.262962e+01                 1.471606e+01                     1.541875e+01                 1.925940e+01                     2.024146e+01
GCLC                                          6.328966e+01                 8.142225e+01                 2.742538e+01                     9.193067e+01                 1.239251e+02                     6.938806e+01
NFYA                                          5.132142e+01                 5.813859e+01                 2.729160e+01                     6.749340e+01                 5.766357e+01                     3.922276e+01
STPG1                                         4.767010e+00                 3.668940e+00                 2.675647e+00                     3.975904e+00                 4.814851e+00                     7.561014e+00
NIPAL3                                        2.413933e+01                 2.067307e+01                 9.364765e+00                     3.558919e+01                 3.324540e+01                     2.953521e+01
LAS1L                                         4.310594e+01                 4.367450e+01                 3.545233e+01                     5.168676e+01                 6.391141e+01                     4.560237e+01
ENPP4                                         4.868436e+00                 4.303949e+00                 6.689118e+00                     4.072878e+00                 6.018563e+00                     4.725634e+00
SEMA3F                                        2.069085e+01                 2.187253e+01                 1.832818e+01                     6.885103e+00                 4.700211e+00                     2.236800e+01
ANKIB1                                        2.454503e+01                 2.871651e+01                 2.675647e+01                     1.086101e+01                 2.264126e+01                     2.425825e+01
CYP51A1                                       6.896950e+00                 8.325672e+00                 8.294506e+00                     3.588011e+00                 5.731965e+00                     1.023887e+01
KRIT1                                         1.318535e+01                 7.902333e+00                 1.551875e+01                     1.037614e+01                 1.180785e+01                     7.167211e+00
RAD52                                         1.369247e+01                 9.242907e+00                 1.324445e+01                     1.086101e+01                 8.311349e+00                     8.112338e+00
MYH16                                         0.000000e+00                 0.000000e+00                 8.026942e-01                     4.848664e-01                 0.000000e+00                     0.000000e+00
BAD                                           2.444360e+01                 3.160933e+01                 5.551968e+01                     3.277697e+01                 2.447549e+01                     5.150941e+01
LAP3                                          4.280166e+01                 3.633662e+01                 6.261014e+01                     2.889804e+01                 2.997818e+01                     4.946163e+01
CD99                                          1.530514e+02                 1.219923e+02                 2.959266e+02                     5.818397e+01                 6.442729e+01                     1.819369e+02
HS3ST1                                        6.694099e+00                 6.208976e+00                 8.160724e+00                     3.781958e+00                 4.700211e+00                     6.222084e+00
AOC1                                          0.000000e+00                 3.175045e+00                 8.026942e-01                     2.424332e+00                 4.470933e+00                     6.615887e+00
WNT16                                         2.028515e+00                 0.000000e+00                 1.070259e+00                     9.697328e-01                 1.146393e-01                     0.000000e+00
HECW1                                         2.332792e+00                 2.822262e-01                 3.076994e+00                     0.000000e+00                 6.878358e-01                     9.451268e-01
MAD1L1                                        5.071287e+00                 1.086571e+01                 9.364765e+00                     1.270350e+01                 9.572382e+00                     5.040676e+00
LASP1                                         2.753709e+02                 2.844840e+02                 3.089035e+02                     3.184602e+02                 2.932473e+02                     2.658169e+02
SNX11                                         1.612669e+01                 1.467576e+01                 2.033492e+01                     2.812225e+01                 2.413157e+01                     2.205296e+01
TMEM176A                                      4.685869e+01                 4.219281e+01                 7.197491e+01                     7.660889e+00                 9.457743e+00                     5.930670e+01
M6PR                                          4.655441e+01                 5.877360e+01                 4.441574e+01                     7.224509e+01                 6.351017e+01                     5.938546e+01
KLHL13                                        7.099802e-01                 7.761220e-01                 2.408082e+00                     4.848664e-01                 4.585572e-01                     2.205296e+00
CYP26B1                                       3.448475e+00                 6.561759e+00                 5.618859e+01                     1.357626e+00                 7.451555e-01                     3.938028e+00
ICA1                                          1.135968e+01                 8.043446e+00                 8.160724e+00                     1.173377e+01                 1.197981e+01                     1.173532e+01
DBNDD1                                        5.476990e+00                 1.199461e+00                 3.344559e+00                     1.454599e+00                 1.375672e+00                     8.663662e-01
ALS2                                          1.906804e+01                 1.912082e+01                 1.806062e+01                     1.968558e+01                 2.189611e+01                     1.677600e+01
CASP10                                        3.641184e+01                 2.659982e+01                 1.859575e+01                     4.208640e+01                 3.078065e+01                     2.347065e+01
CFLAR                                         2.517387e+02                 2.868829e+02                 2.382664e+02                     2.551367e+02                 2.732428e+02                     2.041474e+02
TFPI                                          3.154341e+01                 2.250754e+01                 1.150528e+01                     7.079049e+00                 8.139391e+00                     1.653972e+01
                          X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte
TSPAN6                                    3.118367e+00                     3.456795e+00                 0.000000e+00                     4.126355e+00                 1.673259e+00                     7.312985e+00
TNMD                                      0.000000e+00                     0.000000e+00                 0.000000e+00                     6.158739e-02                 2.151333e+00                     0.000000e+00
DPM1                                      1.214522e+01                     7.277462e+00                 5.978896e+00                     9.853982e+00                 1.338607e+01                     1.994451e+00
SCYL3                                     4.431363e+00                     3.638731e+00                 4.982413e+00                     4.372705e+00                 7.410146e+00                     6.648168e+00
C1orf112                                  3.036305e+00                     1.637429e+00                 1.494724e+00                     4.126355e+00                 7.171109e-01                     0.000000e+00
FGR                                       1.029061e+02                     1.357247e+02                 1.320339e+02                     2.084117e+02                 1.644574e+02                     3.590011e+01
CFH                                       3.692803e+00                     7.277462e-01                 0.000000e+00                     4.126355e+00                 0.000000e+00                     0.000000e+00
FUCA2                                     1.395059e+01                     8.551018e+00                 1.046307e+01                     1.995431e+01                 1.338607e+01                     6.648168e-01
GCLC                                      4.931943e+01                     6.222230e+01                 6.975378e+01                     1.180630e+02                 5.593465e+01                     6.382242e+01
NFYA                                      4.012846e+01                     3.766087e+01                 5.231534e+01                     4.268006e+01                 4.828547e+01                     5.318535e+00
STPG1                                     4.677550e+00                     7.277462e-01                 4.982413e-01                     4.988579e+00                 4.063628e+00                     0.000000e+00
NIPAL3                                    1.944876e+01                     2.965566e+01                 3.238569e+01                     2.315686e+01                 1.195185e+01                     1.063707e+01
LAS1L                                     5.432523e+01                     5.530871e+01                 4.533996e+01                     5.000896e+01                 4.183147e+01                     5.318535e+01
ENPP4                                     4.923737e+00                     2.365175e+00                 0.000000e+00                     3.202544e+00                 8.605331e+00                     0.000000e+00
SEMA3F                                    2.601374e+01                     3.602344e+01                 1.145955e+01                     1.866098e+01                 2.509888e+01                     6.116315e+01
ANKIB1                                    2.240300e+01                     2.783629e+01                 1.594372e+01                     2.254098e+01                 2.629407e+01                     1.462597e+01
CYP51A1                                   9.273038e+00                     2.001302e+00                 1.992965e+00                     5.234928e+00                 5.497850e+00                     1.196670e+01
KRIT1                                     5.580235e+00                     9.824574e+00                 9.964826e+00                     1.040827e+01                 1.147377e+01                     8.642619e+00
RAD52                                     1.066810e+01                     7.459399e+00                 3.985930e+00                     1.281018e+01                 4.302665e+00                     1.130189e+01
MYH16                                     2.461869e-01                     0.000000e+00                 0.000000e+00                     0.000000e+00                 0.000000e+00                     0.000000e+00
BAD                                       3.725628e+01                     3.529569e+01                 2.341734e+01                     3.085528e+01                 3.083577e+01                     2.725749e+01
LAP3                                      4.259033e+01                     5.712808e+01                 5.530479e+01                     4.169466e+01                 6.119346e+01                     1.861487e+01
CD99                                      1.816038e+02                     1.530086e+02                 1.609319e+02                     1.299494e+02                 1.565692e+02                     3.231010e+02
HS3ST1                                    3.774865e+00                     2.365175e+00                 2.491207e+00                     1.108573e+00                 5.736887e+00                     0.000000e+00
AOC1                                      1.477121e+00                     7.459399e+00                 6.477137e+00                     3.140957e+00                 1.673259e+00                     0.000000e+00
WNT16                                     7.385606e-01                     1.819366e-01                 0.000000e+00                     0.000000e+00                 0.000000e+00                     0.000000e+00
HECW1                                     2.708055e+00                     1.091619e+00                 2.989448e+00                     1.108573e+00                 0.000000e+00                     0.000000e+00
MAD1L1                                    7.057357e+00                     1.473686e+01                 3.487689e+00                     8.252710e+00                 1.912296e+00                     3.124639e+01
LASP1                                     2.670307e+02                     3.080186e+02                 2.795134e+02                     2.370499e+02                 2.968839e+02                     1.715227e+02
SNX11                                     8.944789e+00                     2.747242e+01                 2.541031e+01                     1.724447e+01                 1.721066e+01                     5.983352e+00
TMEM176A                                  4.579076e+01                     2.674467e+01                 1.494724e+01                     5.130230e+01                 5.928117e+01                     1.728524e+01
M6PR                                      5.933103e+01                     3.966217e+01                 4.683468e+01                     6.682232e+01                 5.784695e+01                     1.529079e+01
KLHL13                                    2.790118e+00                     2.910985e+00                 0.000000e+00                     2.648258e+00                 1.195185e+00                     0.000000e+00
CYP26B1                                   6.400858e+00                     8.914891e+00                 9.964826e+00                     1.348764e+01                 1.816681e+01                     3.855938e+01
ICA1                                      5.005799e+00                     8.187145e+00                 4.982413e-01                     9.915570e+00                 1.864488e+01                     2.659267e+00
DBNDD1                                    1.641246e+00                     3.638731e-01                 4.982413e-01                     6.158739e-01                 0.000000e+00                     0.000000e+00
ALS2                                      1.731514e+01                     1.455492e+01                 1.444900e+01                     2.352638e+01                 1.266896e+01                     5.318535e+00
CASP10                                    3.085542e+01                     2.747242e+01                 3.288393e+01                     2.494289e+01                 1.744970e+01                     3.988901e+00
CFLAR                                     2.685899e+02                     3.198445e+02                 3.771687e+02                     3.003001e+02                 3.093138e+02                     3.217714e+02
TFPI                                      2.289538e+01                     1.655623e+01                 8.968344e+00                     2.420384e+01                 2.246947e+01                     1.329634e+00
                          X158_Hip_sclerotic_adipocyte
TSPAN6                                    1.170541e+01
TNMD                                      0.000000e+00
DPM1                                      1.486904e+01
SCYL3                                     8.858149e+00
C1orf112                                  2.372718e+00
FGR                                       3.622350e+01
CFH                                       2.689081e+00
FUCA2                                     1.534358e+01
GCLC                                      4.017803e+01
NFYA                                      4.081076e+01
STPG1                                     1.328722e+01
NIPAL3                                    1.043996e+01
LAS1L                                     4.682164e+01
ENPP4                                     3.163625e-01
SEMA3F                                    3.606532e+01
ANKIB1                                    4.049439e+01
CYP51A1                                   2.293628e+01
KRIT1                                     1.233814e+01
RAD52                                     8.383605e+00
MYH16                                     1.107269e+00
BAD                                       1.692539e+01
LAP3                                      8.462696e+01
CD99                                      2.741281e+02
HS3ST1                                    3.638168e+00
AOC1                                      1.581812e-01
WNT16                                     1.423631e+00
HECW1                                     1.739993e+00
MAD1L1                                    6.801793e+00
LASP1                                     2.303119e+02
SNX11                                     1.028178e+01
TMEM176A                                  8.288696e+01
M6PR                                      4.444892e+01
KLHL13                                    6.327249e-01
CYP26B1                                   2.878898e+01
ICA1                                      6.327249e+00
DBNDD1                                    4.745437e-01
ALS2                                      2.167083e+01
CASP10                                    1.154723e+01
CFLAR                                     2.560954e+02
TFPI                                      3.685623e+01
 [ reached getOption("max.print") -- omitted 21583 rows ]

$hip_adipocytes_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158    groupHSA
TSPAN6     -12.15943  -0.5473984  -0.4598270  -1.2795340  -0.2222066 -0.56536356  -0.3725572   0.4329859  -2.0090604  -0.6402360  -1.0044140 -0.58670075  0.56115060  0.07575426
TNMD       -13.75752  -2.7835830  -0.9877961  -1.6904182  -1.8703239 -1.39395901  -1.6016356  -4.2275126  -4.1825180  -2.4168712  -4.1527976 -0.06935854 -4.20411251  0.10752944
DPM1       -11.19366  -0.4478492  -0.4475518  -0.7353736   0.1623264 -0.05665869  -0.1610301  -0.2694277  -0.4567248  -0.2700309  -0.7532161 -0.21623167 -0.48227961  0.08019759
SCYL3      -12.65366  -0.3197865   0.4627620  -0.3045499   0.3236600  0.51192455   0.2736772   0.4375748   0.4001212   0.4405716   0.4688902  0.80682697  1.08954615 -0.31037889
C1orf112   -13.68441   0.7768264  -4.2462710   0.9060191   0.0522886 -0.05655976   1.0689917  -0.4666419   0.7090236   0.6955757   0.2736322  0.76285920  0.07292938  0.13698081
21618 more rows ...

$fitted.values
         X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte
TSPAN6                          26.441999                    36.871075                       21.2825584                   32.2065693                     1.547709e+01                 9.701243e+00
TNMD                             5.284546                     7.598621                        0.3520143                    0.5493088                     1.783334e+00                 1.152674e+00
DPM1                            69.698907                    97.292244                       62.0255497                   93.9619428                     4.142678e+01                 2.599442e+01
SCYL3                           16.107646                    15.181954                       16.2801150                   16.6526051                     2.388391e+01                 1.011923e+01
C1orf112                         5.687384                     8.440004                       17.3838927                   27.9966617                     1.256013e-07                 8.378591e-08
         X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6                          4.1958780                     8.670562                        6.1706255                   17.0665864                        26.407811                    9.4291988
TNMD                            0.5251942                     1.119128                        0.2191603                    0.6250502                         2.210797                    0.8140047
DPM1                           19.2069789                    39.732343                       23.9067648                   66.1910112                       116.024601                   41.4718313
SCYL3                           6.8265325                     9.535174                        6.5051807                   12.1613258                        47.478641                   11.4589482
C1orf112                        8.1809948                    17.991571                        1.7476155                    5.1440116                         9.443718                    3.5885914
         X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte
TSPAN6                          35.365255                    55.028002                 6.500000e+01                     7.059030e+00                 1.292676e+01                       34.7909482
TNMD                             1.940472                     3.113508                 3.164652e-08                     4.228408e-08                 7.984672e-08                        0.9912198
DPM1                           115.331055                   179.644509                 8.500000e+01                     8.970438e+01                 1.644444e+02                      133.1604158
SCYL3                           41.276692                    43.412612                 2.700000e+01                     4.903510e+01                 6.069540e+01                       62.8604307
C1orf112                        32.524353                    53.858493                 6.000000e+00                     2.365971e+01                 4.610973e+01                       28.7410358
         X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte
TSPAN6                      36.143278                     1.045605e+01                 4.132796e+00                         46.99817                    13.107014                     1.375748e+01
TNMD                         1.061859                     2.227037e-08                 9.076937e-09                         15.74840                     4.528922                     6.400858e-09
DPM1                       138.483219                     3.552243e+01                 1.405529e+01                        179.71728                    50.173380                     1.275515e+01
SCYL3                       44.141055                     2.799564e+01                 7.479468e+00                        116.10763                    21.887070                     1.428007e+01
C1orf112                    31.776223                     8.135061e+00                 3.421966e+00                         39.41571                    11.698515                     1.815832e+00
         X158_Hip_sclerotic_adipocyte
TSPAN6                   6.258668e+01
TNMD                     3.002735e-08
DPM1                     5.808839e+01
SCYL3                    4.391144e+01
C1orf112                 8.791386e+00
21618 more rows ...

$deviance
[1] 26.195847  7.090188  8.490570 12.459343  9.061801
21618 more elements ...

$iter
[1] 11 18  6  9 18
21618 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
21618 more elements ...

$method
[1] "levenberg"

$counts
         X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte
TSPAN6                                 30                           32                               35                           12                                0                           20
TNMD                                    5                            8                                0                            1                                2                            1
DPM1                                   67                          101                               91                           51                               52                           19
SCYL3                                  30                            2                               13                           20                               22                           11
C1orf112                                6                            8                               25                           16                                0                            0
         X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6                                  0                           16                               10                            8                               30                            8
TNMD                                    0                            2                                0                            1                                4                            0
DPM1                                   18                           42                               18                           81                              112                           43
SCYL3                                   8                            8                                9                            8                               86                            1
C1orf112                               14                            6                                0                            9                                4                            6
         X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte
TSPAN6                                 38                           51                           65                                1                           23                               33
TNMD                                    4                            0                            0                                0                            0                                2
DPM1                                  119                          174                           85                              115                          119                              124
SCYL3                                  35                           50                           27                               26                           89                               49
C1orf112                               41                           40                            6                               19                           55                               24
         X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte
TSPAN6                             38                               19                            0                               67                            7                               11
TNMD                                0                                0                            0                                1                            9                                0
DPM1                              148                               40                           12                              160                           56                                3
SCYL3                              54                               20                           10                               71                           31                               10
C1orf112                           37                                9                            3                               67                            3                                0
         X158_Hip_sclerotic_adipocyte
TSPAN6                             74
TNMD                                0
DPM1                               94
SCYL3                              56
C1orf112                           15
21618 more rows ...

$unshrunk.coefficients
         (Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157  patientX158    groupHSA
TSPAN6     -12.16412  -0.5489509  -0.4635492  -1.2886140 -0.22261836 -0.56764256  -0.3740848   0.4322601  -2.0303984  -0.6433719  -1.0083028 -0.58857573   0.56195233  0.07919987
TNMD       -13.77429  -3.0407553  -1.0142583  -1.7565369 -1.95020357 -1.43778230  -1.6667164 -19.4313043 -19.3533944  -2.5913812 -19.3653254 -0.07177878 -19.31629685  0.10990627
DPM1       -11.19489  -0.4485234  -0.4482134  -0.7366739  0.16251188 -0.05673116  -0.1612390  -0.2697678  -0.4574175  -0.2704057  -0.7545501 -0.21653053  -0.48292611  0.08026075
SCYL3      -12.65978  -0.3212348   0.4659547  -0.3062402  0.32583988  0.51463711   0.2761429   0.4410296   0.4034899   0.4438473   0.4722246  0.81149270   1.09489458 -0.31246045
C1orf112   -13.70083   0.7854085 -17.5563597   0.9158003  0.05253689 -0.05924937   1.0788777  -0.4759231   0.7157706   0.7022999   0.2774029  0.77218323   0.07361686  0.14145851
21618 more rows ...

$df.residual
[1] 11 11 11 11 11
21618 more elements ...

$design
                                 (Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 groupHSA
X108_Hip_non.sclerotic_adipocyte           1           0           0           0           0           0           0           0           0           0           0           0           0        0
X108_Hip_sclerotic_adipocyte               1           0           0           0           0           0           0           0           0           0           0           0           0        1
X125_Hip_non.sclerotic_adipocyte           1           1           0           0           0           0           0           0           0           0           0           0           0        0
X125_Hip_sclerotic_adipocyte               1           1           0           0           0           0           0           0           0           0           0           0           0        1
X126_Hip_non.sclerotic_adipocyte           1           0           1           0           0           0           0           0           0           0           0           0           0        0
20 more rows ...

$offset
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 15.43908 15.69235 15.77096 16.10605 15.36703 14.82073 14.88684 15.53347 14.20654 15.14467 16.00543 14.89638 16.10394 16.46685 15.82705 16.14883 16.67462 16.35685 16.31579 15.51961 14.51218 16.60281 15.24665 14.22375
        [,25]
[1,] 15.65952
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 25
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
21618 more rows ...

$dispersion
[1] 0.5576023 2.8420737 0.2406457 0.5091346 0.9366525
21618 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  1.9934747 -0.8832058  3.4645637  2.1348337  1.1490553
21618 more elements ...

$df.residual.zeros
[1] 11  8 11 11 10
21618 more elements ...

$df.prior
[1] 19.72888 19.72888 19.72888 19.72888 19.72888
21618 more elements ...

$var.post
[1] 1.6937166 1.3084838 0.9635258 1.2365193 1.2100764
21618 more elements ...

$var.prior
[1] 1.310270 1.479689 1.070385 1.294423 1.364113
21618 more elements ...

$samples
20 more rows ...

$genes
21618 more rows ...


$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.9090058

$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.994568

$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.490907

$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 4.021385


$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.812784 2.812784

$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 3.689862 3.358340



$hip_adipocytes_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$hip_adipocytes_sclerotic_vs_non_sclerotic$boxplot_gg


$hip_pellet_sclerotic_vs_non_sclerotic
$hip_pellet_sclerotic_vs_non_sclerotic$name
[1] "HSP-vs-HNSP"

$hip_pellet_sclerotic_vs_non_sclerotic$results
Coefficient:  groupHSP 

$hip_pellet_sclerotic_vs_non_sclerotic$colsums_samples

$hip_pellet_sclerotic_vs_non_sclerotic$normalized_matrix
                          X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet
TSPAN6                                     3.705423e+00              3.922387e+00                  1.691089e+00              8.441617e-01                  0.000000e+00              0.000000e+00
DPM1                                       1.667441e+01              2.603038e+01                  1.050891e+01              1.786809e+01                  9.512169e-01              6.216233e+00
SCYL3                                      9.263559e+00              3.565806e-01                  4.831682e+00              5.346357e+00                  1.331704e+01              6.216233e+00
C1orf112                                   6.484491e+00              0.000000e+00                  4.831682e+00              4.502196e+00                  0.000000e+00              8.288311e+00
FGR                                        2.223254e+02              2.674354e+02                  4.383543e+02              4.727305e+02                  1.398289e+02              7.355876e+01
CFH                                        5.558135e+00              3.565806e-01                  3.623761e-01              1.125549e+00                  0.000000e+00              3.108117e+00
FUCA2                                      2.779068e+00              1.426322e+01                  1.207920e+01              8.723004e+00                  2.853651e+00              1.295049e+01
GCLC                                       2.223254e+01              2.460406e+01                  8.407126e+01              6.767363e+01                  1.046339e+01              1.502256e+01
NFYA                                       3.612788e+01              5.206077e+01                  7.549503e+01              4.825791e+01                  2.378042e+01              2.641899e+01
STPG1                                      2.779068e+00              4.278967e+00                  5.798018e+00              6.331212e+00                  4.756084e+00              5.180194e-01
NIPAL3                                     9.263559e+00              2.282116e+01                  1.763564e+01              1.378797e+01                  3.234137e+01              1.761266e+01
LAS1L                                      5.836042e+01              6.204502e+01                  6.607325e+01              4.530334e+01                  5.136571e+01              4.506769e+01
ENPP4                                      7.410847e+00              1.176716e+01                  3.140593e+00              4.502196e+00                  0.000000e+00              1.036039e+00
SEMA3F                                     3.705423e+01              4.278967e+01                  1.932673e+00              1.421005e+01                  3.899989e+01              5.491006e+01
ANKIB1                                     8.337203e+00              1.604613e+01                  1.872277e+01              1.533560e+01                  2.473164e+01              3.367126e+01
CYP51A1                                    8.337203e+00              1.212374e+01                  6.039602e+00              5.487051e+00                  7.609735e+00              7.252272e+00
KRIT1                                      3.705423e+00              3.209225e+00                  1.727326e+01              1.027063e+01                  8.560952e+00              6.734253e+00
RAD52                                      1.111627e+01              1.069742e+01                  1.775643e+01              8.019536e+00                  9.512169e-01              1.295049e+01
MYH16                                      0.000000e+00              0.000000e+00                  2.415841e-01              0.000000e+00                  0.000000e+00              0.000000e+00
BAD                                        1.667441e+01              1.426322e+01                  1.691089e+01              1.674254e+01                  1.141460e+01              2.175682e+01
LAP3                                       2.315890e+01              3.066593e+01                  3.961979e+01              4.192670e+01                  1.027314e+02              6.268035e+01
CD99                                       1.232053e+02              1.757942e+02                  6.691879e+01              1.058016e+02                  2.577798e+02              2.792125e+02
HS3ST1                                     8.337203e+00              1.961193e+01                  0.000000e+00              5.768438e+00                  1.331704e+01              1.916672e+01
AOC1                                       0.000000e+00              0.000000e+00                  2.415841e+00              2.110404e+00                  0.000000e+00              0.000000e+00
WNT16                                      0.000000e+00              3.387516e+01                  0.000000e+00              1.899364e+01                  0.000000e+00              0.000000e+00
HECW1                                      0.000000e+00              5.705290e+00                  1.087128e+00              0.000000e+00                  9.512169e+00              8.288311e+00
MAD1L1                                     6.484491e+00              1.426322e+01                  1.135445e+01              1.238104e+01                  2.092677e+01              9.842369e+00
LASP1                                      1.806394e+02              1.921969e+02                  1.485742e+02              1.938758e+02                  2.435115e+02              2.072078e+02
SNX11                                      1.482169e+01              8.914515e+00                  1.425346e+01              1.392867e+01                  1.807312e+01              7.770291e+00
TMEM176A                                   1.389534e+01              8.914515e+00                  1.062970e+01              9.848553e+00                  3.519502e+01              4.195957e+01
M6PR                                       2.964339e+01              3.173567e+01                  6.426137e+01              3.742450e+01                  3.043894e+01              3.626136e+01
KLHL13                                     0.000000e+00              1.426322e+00                  2.415841e+00              1.547630e+00                  9.512169e-01              1.554058e+00
CYP26B1                                    6.577127e+01              5.740948e+01                  1.328713e+00              1.027063e+01                  2.758529e+01              6.837856e+01
ICA1                                       1.389534e+01              4.278967e+00                  1.014653e+01              7.738149e+00                  0.000000e+00              1.502256e+01
DBNDD1                                     0.000000e+00              0.000000e+00                  1.691089e+00              2.391791e+00                  0.000000e+00              0.000000e+00
ALS2                                       2.037983e+01              4.992128e+00                  1.968910e+01              1.069271e+01                  3.804867e+01              2.486493e+01
CASP10                                     1.018991e+01              1.212374e+01                  2.838613e+01              2.532485e+01                  2.568286e+01              3.522532e+01
CFLAR                                      2.955075e+02              3.683478e+02                  4.180613e+02              4.134985e+02                  4.708523e+02              3.538073e+02
                          X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet
TSPAN6                                     0.000000e+00              2.421970e-01                  8.271076e-01              6.832711e-01              0.000000e+00                  1.095086e+00              2.258421e+00
DPM1                                       5.095465e+00              1.582354e+01                  2.135441e+01              4.099627e+00              1.214842e+00                  8.291366e+00              1.219547e+01
SCYL3                                      0.000000e+00              3.794420e+00                  3.383622e+00              1.184337e+01              9.718734e+00                  1.251527e+00              2.408982e+00
C1orf112                                   1.019093e+01              1.453182e+00                  3.985155e+00              2.277570e-01              0.000000e+00                  5.631871e+00              3.914596e+00
FGR                                        7.199164e+02              3.657175e+02                  3.966357e+02              4.987879e+01              3.097846e+01                  1.907014e+02              3.628529e+02
CFH                                        7.279235e-01              2.421970e-01                  3.759580e-01              7.743739e+00              4.251946e+00                  1.095086e+00              0.000000e+00
FUCA2                                      6.551312e+00              1.396669e+01                  1.609100e+01              1.480421e+01              2.672652e+01                  1.079442e+01              1.851905e+01
GCLC                                       6.114558e+01              3.786346e+01                  6.970261e+01              3.416356e+01              2.065231e+01                  6.992907e+01              7.497957e+01
NFYA                                       4.221956e+01              5.715849e+01                  6.143154e+01              2.755860e+01              2.854878e+01                  3.770225e+01              6.278410e+01
STPG1                                      1.383055e+01              2.179773e+00                  2.330940e+00              1.594299e+00              3.037104e+00                  5.944753e+00              2.107859e+00
NIPAL3                                     1.455847e+01              3.616808e+01                  2.691859e+01              2.140916e+01              2.368941e+01                  2.549986e+01              2.559544e+01
LAS1L                                      6.041765e+01              5.158796e+01                  4.857377e+01              3.780767e+01              2.611910e+01                  4.364700e+01              3.462912e+01
ENPP4                                      1.455847e+00              6.781516e+00                  5.564178e+00              0.000000e+00              0.000000e+00                  1.720850e+00              3.161789e+00
SEMA3F                                     2.183771e+00              8.073233e+00                  4.060346e+00              2.801412e+01              5.223820e+01                  1.517476e+01              8.732560e+00
ANKIB1                                     8.007159e+00              1.550061e+01                  1.481275e+01              2.391449e+01              1.761521e+01                  1.533121e+01              2.017523e+01
CYP51A1                                    7.279235e+00              7.669571e+00                  1.165470e+01              1.548748e+01              1.154100e+01                  6.414076e+00              8.431438e+00
KRIT1                                      1.965394e+01              9.768612e+00                  1.661734e+01              4.327384e+00              3.037104e+00                  8.917130e+00              5.871894e+00
RAD52                                      6.551312e+00              1.219058e+01                  1.255700e+01              7.515982e+00              4.859367e+00                  1.032510e+01              6.925824e+00
MYH16                                      0.000000e+00              0.000000e+00                  8.271076e-01              0.000000e+00              3.037104e+00                  0.000000e+00              7.528069e-01
BAD                                        1.674224e+01              1.961796e+01                  2.045212e+01              3.553010e+01              6.499403e+01                  4.223903e+01              3.643586e+01
LAP3                                       2.183771e+01              3.762127e+01                  2.684340e+01              2.118140e+01              3.583783e+01                  3.253970e+01              4.652347e+01
CD99                                       4.149164e+01              1.713140e+02                  9.323758e+01              2.480274e+02              3.711342e+02                  9.574181e+01              1.187929e+02
HS3ST1                                     4.367541e+00              7.023713e+00                  4.661879e+00              2.095365e+01              1.883005e+01                  1.048154e+01              1.806737e+00
AOC1                                       0.000000e+00              4.843940e-01                  1.052682e+00              1.138785e+00              3.644525e+00                  1.407968e+00              1.806737e+00
WNT16                                      0.000000e+00              8.880556e-01                  6.015328e-01              5.693926e+00              2.125973e+01                  0.000000e+00              4.968526e+00
HECW1                                      1.091885e+01              4.036617e-01                  2.255748e-01              1.366542e+00              2.429684e+00                  1.095086e+00              6.022455e-01
MAD1L1                                     5.823388e+00              1.324010e+01                  1.609100e+01              9.338038e+00              7.289051e+00                  1.220239e+01              9.635929e+00
LASP1                                      1.128281e+02              2.354155e+02                  1.897084e+02              2.521270e+02              2.277828e+02                  2.384159e+02              2.371342e+02
SNX11                                      1.310262e+01              1.889137e+01                  1.970020e+01              1.730953e+01              2.794136e+01                  2.018087e+01              2.107859e+01
TMEM176A                                   0.000000e+00              2.898291e+01                  7.443968e+00              7.515982e+01              3.340815e+01                  2.190172e+01              2.996172e+01
M6PR                                       1.528639e+01              4.367619e+01                  4.797224e+01              2.801412e+01              2.247457e+01                  4.302124e+01              6.805375e+01
KLHL13                                     8.007159e+00              4.843940e-01                  6.015328e-01              1.138785e+00              6.074209e-01                  1.720850e+00              2.860666e+00
CYP26B1                                    0.000000e+00              9.768612e+00                  1.954982e+00              5.010655e+01              8.382408e+01                  3.598140e+00              9.334806e+00
ICA1                                       1.164678e+01              9.122753e+00                  1.684292e+01              4.327384e+00              6.074209e-01                  8.134925e+00              7.979754e+00
DBNDD1                                     5.823388e+00              2.018308e+00                  1.203066e+00              3.188598e+00              7.896471e+00                  3.128817e-01              2.107859e+00
ALS2                                       1.310262e+01              1.784185e+01                  1.556466e+01              2.573654e+01              1.822263e+01                  1.548765e+01              1.189435e+01
CASP10                                     1.965394e+01              2.777192e+01                  6.090520e+01              2.505327e+01              8.503892e+00                  4.161327e+01              3.944708e+01
CFLAR                                      3.006324e+02              5.315417e+02                  4.237047e+02              2.393726e+02              1.779743e+02                  2.632900e+02              3.687248e+02
                          X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet
TSPAN6                                     0.000000e+00              2.427193e+00                  6.589087e-01              7.708632e-01                  3.647412e-01              9.909671e-01                   0.00000
DPM1                                       2.138737e+01              9.708770e+00                  1.479550e+01              8.993404e+00                  1.568387e+01              1.172644e+01                   9.31312
SCYL3                                      0.000000e+00              1.213596e+01                  4.193055e+00              5.652997e+00                  3.793308e+00              4.129030e+00                   0.00000
C1orf112                                   0.000000e+00              8.090642e-01                  3.893551e+00              4.882133e+00                  2.115499e+00              1.486451e+00                   0.00000
FGR                                        1.168080e+02              2.831725e+01                  2.363685e+02              2.507875e+02                  3.456288e+02              3.446914e+02                 181.60584
CFH                                        0.000000e+00              2.427193e+01                  5.990079e-02              1.798681e+00                  1.531913e+00              2.312257e+00                  11.64140
FUCA2                                      8.225912e+00              2.427193e+01                  1.311827e+01              1.207686e+01                  1.451670e+01              1.123096e+01                  10.47726
GCLC                                       1.069369e+01              2.669912e+01                  1.071026e+02              5.473129e+01                  9.140414e+01              6.978060e+01                  15.13382
NFYA                                       3.619401e+01              6.553420e+01                  5.037656e+01              4.471006e+01                  5.164735e+01              4.219868e+01                  32.59592
STPG1                                      4.112956e+00              6.472513e+00                  6.169781e+00              1.541726e+00                  4.668687e+00              4.046449e+00                   0.00000
NIPAL3                                     1.645182e+00              2.669912e+01                  2.845288e+01              3.571666e+01                  3.063826e+01              2.361805e+01                  57.04286
LAS1L                                      4.688770e+01              4.611666e+01                  7.098244e+01              4.445311e+01                  5.967166e+01              6.928512e+01                  68.68426
ENPP4                                      5.758139e+00              3.236257e+00                  2.815337e+00              5.139088e+00                  1.677810e+00              1.238709e+00                   0.00000
SEMA3F                                     3.701661e+01              2.912631e+01                  3.893551e+00              7.451677e+00                  4.522791e+00              4.129030e+00                  29.10350
ANKIB1                                     4.112956e+00              3.155350e+01                  1.904845e+01              1.156295e+01                  1.685104e+01              2.105805e+01                   2.32828
CYP51A1                                    4.112956e+00              1.132690e+01                  6.708888e+00              1.259077e+01                  4.376894e+00              9.496768e+00                   9.31312
KRIT1                                      1.809701e+01              4.045321e+00                  1.515490e+01              8.736449e+00                  9.920961e+00              9.083865e+00                  13.96968
RAD52                                      7.403321e+00              1.294503e+01                  1.485540e+01              7.965586e+00                  1.911244e+01              1.725934e+01                  19.79038
MYH16                                      0.000000e+00              0.000000e+00                  0.000000e+00              0.000000e+00                  0.000000e+00              0.000000e+00                   0.00000
BAD                                        2.056478e+01              6.067981e+01                  1.862915e+01              2.389676e+01                  2.027961e+01              2.089289e+01                  18.62624
LAP3                                       2.056478e+01              8.899706e+01                  2.839297e+01              2.312590e+01                  1.794527e+01              2.873805e+01                  25.61108
CD99                                       2.656970e+02              3.406160e+02                  7.421708e+01              6.398164e+01                  8.009717e+01              9.430703e+01                 225.84316
HS3ST1                                     4.935547e+00              2.103567e+01                  1.916825e+00              2.055635e+00                  4.158050e+00              2.725159e+00                  34.92420
AOC1                                       0.000000e+00              0.000000e+00                  5.990079e-01              0.000000e+00                  1.750758e+00              1.156128e+00                   0.00000
WNT16                                      0.000000e+00              4.530759e+01                  0.000000e+00              1.798681e+00                  0.000000e+00              1.734192e+00                   4.65656
HECW1                                      1.645182e+00              4.045321e+00                  2.396032e-01              7.708632e-01                  5.835859e-01              9.083865e-01                   0.00000
MAD1L1                                     9.048504e+00              3.317163e+01                  1.922815e+01              1.310467e+01                  1.232825e+01              1.494709e+01                   9.31312
LASP1                                      2.204545e+02              2.144020e+02                  1.900652e+02              1.793542e+02                  1.879147e+02              2.067818e+02                 109.42916
SNX11                                      1.645182e+00              1.051783e+01                  1.617321e+01              1.490335e+01                  1.612156e+01              1.486451e+01                   0.00000
TMEM176A                                   3.701661e+01              7.686110e+01                  5.151468e+00              2.363980e+01                  2.261395e+00              5.367738e+00                   3.49242
M6PR                                       4.359734e+01              6.715233e+01                  4.977756e+01              3.545971e+01                  5.456528e+01              5.086964e+01                  47.72974
KLHL13                                     2.467774e+00              0.000000e+00                  7.188095e-01              5.139088e-01                  8.024306e-01              6.606447e-01                   0.00000
CYP26B1                                    1.233887e+01              3.478976e+01                  1.257917e+00              8.479495e+00                  1.458965e-01              7.267092e+00                  75.66910
ICA1                                       8.225912e+00              0.000000e+00                  9.284622e+00              8.479495e+00                  1.371427e+01              1.593805e+01                  13.96968
DBNDD1                                     8.225912e-01              4.854385e+00                  1.737123e+00              2.055635e+00                  5.471118e+00              7.101931e+00                   0.00000
ALS2                                       7.403321e+00              4.207134e+01                  1.725143e+01              1.695899e+01                  2.779328e+01              2.378321e+01                  13.96968
CASP10                                     6.580730e+00              8.899706e+00                  2.935139e+01              2.723717e+01                  4.530086e+01              5.260384e+01                  32.59592
CFLAR                                      2.986006e+02              8.899706e+01                  2.935139e+02              2.410232e+02                  4.377624e+02              4.195094e+02                 168.80030
                          X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                                     0.000000e+00              0.000000e+00                  3.208281e+00              8.262523e+00                 3.958206e+00             9.413219e+00
DPM1                                       1.208301e+01              9.309130e+00                  1.094590e+01              9.584527e+00                 1.741611e+01             2.235639e+01
SCYL3                                      2.066831e+00              3.324689e+00                  5.095506e+00              4.957514e+00                 2.691580e+00             1.176652e+00
C1orf112                                   4.133663e+00              8.865838e-01                  5.661673e-01              9.915028e-01                 4.749848e-01             2.059142e+00
FGR                                        4.273572e+02              3.799012e+02                  1.560734e+02              1.305479e+02                 9.908182e+02             4.471279e+01
CFH                                        0.000000e+00              1.773168e+00                  3.963171e+00              8.923525e+00                 6.333130e-01             8.824893e+00
FUCA2                                      2.098629e+01              1.751003e+01                  1.037973e+01              1.454204e+01                 1.139963e+01             2.794549e+01
GCLC                                       6.645658e+01              3.502006e+01                  7.926342e+01              2.776208e+01                 4.528188e+01             1.764979e+01
NFYA                                       3.688499e+01              5.053528e+01                  4.246255e+01              3.635510e+01                 5.842313e+01             2.088558e+01
STPG1                                      3.338728e+00              2.881397e+00                  7.548897e+00              3.635510e+00                 5.066504e+00             2.353305e+00
NIPAL3                                     2.448400e+01              1.795332e+01                  2.019330e+01              5.949017e+00                 2.137431e+01             3.206378e+01
LAS1L                                      6.375380e+01              3.745817e+01                  3.359259e+01              4.032111e+01                 5.446492e+01             3.765288e+01
ENPP4                                      3.020754e+00              3.324689e+00                  1.509779e+00              2.313506e+00                 3.958206e+00             8.824893e-01
SEMA3F                                     2.384806e+00              1.928320e+01                  2.434519e+01              3.404159e+01                 1.504118e+01             2.647468e+01
ANKIB1                                     1.748857e+01              9.087484e+00                  1.868352e+01              2.280456e+01                 9.816352e+00             1.647313e+01
CYP51A1                                    1.081112e+01              1.352040e+01                  1.962713e+01              8.923525e+00                 1.060799e+01             6.471588e+00
KRIT1                                      7.949352e+00              6.871025e+00                  1.019101e+01              5.949017e+00                 5.699817e+00             6.765751e+00
RAD52                                      1.033416e+01              7.092671e+00                  1.132335e+01              8.593024e+00                 1.171629e+01             2.294472e+01
MYH16                                      1.271896e+00              0.000000e+00                  0.000000e+00              3.635510e+00                 0.000000e+00             1.176652e+00
BAD                                        1.383187e+01              2.726245e+01                  2.094819e+01              2.710108e+01                 2.549085e+01             3.912369e+01
LAP3                                       2.353008e+01              3.457677e+01                  2.755347e+01              4.230412e+01                 2.248261e+01             3.471124e+01
CD99                                       1.195583e+02              1.540439e+02                  1.717374e+02              1.735130e+02                 9.293869e+01             5.174329e+02
HS3ST1                                     1.430883e+00              3.324689e+00                  1.434290e+01              1.024553e+01                 5.858145e+00             2.941631e+00
AOC1                                       9.221248e+00              3.103043e+00                  0.000000e+00              1.983006e+00                 0.000000e+00             1.176652e+00
WNT16                                      0.000000e+00              8.200901e+00                  1.773991e+01              5.056664e+01                 6.491458e+00             4.706609e+00
HECW1                                      0.000000e+00              0.000000e+00                  0.000000e+00              1.983006e+00                 2.216596e+00             4.118283e+00
MAD1L1                                     1.637566e+01              1.374205e+01                  1.245568e+01              1.024553e+01                 9.816352e+00             1.264901e+01
LASP1                                      1.860148e+02              2.243057e+02                  1.809848e+02              1.738435e+02                 3.005070e+02             2.803374e+02
SNX11                                      1.573972e+01              1.773168e+01                  1.283313e+01              8.593024e+00                 1.567450e+01             9.119056e+00
TMEM176A                                   3.736195e+01              8.489040e+01                  9.813566e+00              7.568471e+01                 4.116535e+00             1.500232e+01
M6PR                                       5.612242e+01              7.380810e+01                  4.887911e+01              3.701610e+01                 4.734015e+01             1.882644e+01
KLHL13                                     0.000000e+00              2.438106e+00                  0.000000e+00              3.305009e-01                 7.916413e-01             8.824893e-01
CYP26B1                                    6.359482e+00              8.422546e+00                  2.189180e+01              2.313506e+01                 2.374924e+00             4.235948e+01
ICA1                                       8.585300e+00              2.438106e+00                  1.132335e+01              5.949017e+00                 1.314125e+01             2.647468e+00
DBNDD1                                     0.000000e+00              4.432919e-01                  5.095506e+00              3.966011e+00                 1.424954e+00             1.176652e+00
ALS2                                       1.717060e+01              1.618016e+01                  1.188951e+01              1.421154e+01                 1.456620e+01             2.912215e+01
CASP10                                     2.623286e+01              2.016978e+01                  2.547753e+01              1.090653e+01                 7.093106e+01             9.119056e+00
CFLAR                                      6.469183e+02              5.221979e+02                  2.700618e+02              2.462232e+02                 7.135854e+02             1.185477e+02
 [ reached getOption("max.print") -- omitted 22508 rows ]

$hip_pellet_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158  patientX79    groupHSP
TSPAN6    -12.740287 -0.98336986  -5.2767541  -3.1422255  -1.5325673  -5.4454023  -0.8824138 -1.31582976 -1.63189193  -1.7990018 -5.44540229  -5.1544555  0.30709634  0.46969393  0.55881924
DPM1      -10.755329 -0.41745530  -1.7118379  -0.6803483  -0.5052503  -2.8647235  -0.7413367 -0.32113750 -0.58240662  -0.4479869 -0.84358389  -0.6945276 -0.73576951 -0.07986831  0.01719896
SCYL3     -12.348296  0.02295286   0.7087225  -0.9030166   0.3438949   0.5208889  -1.0267619  0.08085371 -0.02403484  -0.2251837 -5.56679921  -0.6350010  0.02161326 -0.86444260  0.28822503
C1orf112  -12.688905  0.61990587   0.6962439   0.6616507  -0.2986155  -4.5559621   0.6157417 -1.72809075  0.57845409  -0.3502281 -4.55596210  -0.1022360 -1.14352517 -0.60870929 -0.38200305
FGR        -8.000193  0.60595429  -0.9363201   0.6858989  -0.3315575  -1.8660556   0.1734696 -1.39878681 -0.02294180   0.3187415 -0.09810122   0.4604965 -0.58345207  0.46473083 -0.51525569
22541 more rows ...

$fitted.values
         X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet
TSPAN6                        3.110785                  14.49617                      8.876079                  13.66936                  7.563447e-09              2.491245e-08                     0.1524839
DPM1                         23.001335                  60.80191                    116.133647                 101.45327                  4.026045e+00              7.522395e+00                    14.8100656
SCYL3                         4.659015                  16.18633                     36.539049                  41.95225                  9.235434e+00              2.267905e+01                     2.3872628
C1orf112                      3.300630                   5.82979                     47.351648                  27.63980                  6.500934e+00              8.116057e+00                     8.1816635
FGR                         362.051467                 561.79572                   5089.661377                2610.00183                  1.382174e+02              1.515948e+02                   914.8616350
         X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6                    2.466183                      8.119172                  4.808088              1.608063e-08                      7.535575                  14.04482                     0.9171965
DPM1                    135.874915                    170.874785                 57.401012              2.000000e+00                     64.823067                  68.53465                    18.7813013
SCYL3                    28.785416                     80.950823                 35.739857              1.600000e+01                      9.792487                  13.60704                     5.6806924
C1orf112                 50.155173                     30.110502                  6.758517              1.882443e-07                     36.399830                  25.71413                     0.6337894
FGR                    4926.989553                   3201.482006                631.301115              5.100000e+01                   2550.025935                1582.59275                   100.6350555
         X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet
TSPAN6                   1.6727331                      9.185144                  3.840835                      6.313026                  10.00317              8.390625e-09                  4.610174e-08
DPM1                    19.4299118                    198.530978                 47.092183                    186.515852                 167.64732              8.000000e+00                  6.685012e+01
SCYL3                    7.7238955                     70.277558                 21.909233                     47.150432                  55.70017              1.654383e-07                  1.431573e+01
C1orf112                 0.4381088                     91.607774                 14.519267                     29.479757                  17.70503              9.822203e-08                  1.736900e+01
FGR                     61.1136700                   5472.050088                761.929042                   6323.678807                3336.52663              1.560000e+02                  3.343405e+03
         X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                5.931744e-08                     20.705406                 21.207903                     29.07056                28.066405
DPM1                  4.879195e+01                     54.036840                 31.396759                    124.23659                68.039921
SCYL3                 1.373250e+01                     23.357490                 17.836557                     11.41194                 8.214169
C1orf112              8.470568e+00                      5.074451                  1.970043                     10.45415                 3.825557
FGR                   1.432448e+03                    991.518645                338.173590                   3371.40322              1083.849320
22541 more rows ...

$deviance
[1]  2.793172 10.384298 16.817280 16.698857 36.603176
22541 more elements ...

$iter
[1] 19  7 17 17 11
22541 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
22541 more elements ...

$method
[1] "levenberg"

$counts
         X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet
TSPAN6                               4                        11                            14                         6                             0                         0                             0
DPM1                                18                        73                            87                       127                             1                        12                             7
SCYL3                               10                         1                            40                        38                            14                        12                             0
C1orf112                             7                         0                            40                        32                             0                        16                            14
FGR                                240                       750                          3629                      3360                           147                       142                           989
         X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6                           3                            11                         3                         0                             7                        15                             0
DPM1                           196                           284                        18                         2                            53                        81                            26
SCYL3                           47                            45                        52                        16                             8                        16                             0
C1orf112                        18                            53                         1                         0                            36                        26                             0
FGR                           4530                          5275                       219                        51                          1219                      2410                           142
         X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet
TSPAN6                           3                            11                         3                             5                        12                         0                             0
DPM1                            12                           247                        35                           215                       142                         8                            76
SCYL3                           15                            70                        22                            52                        50                         0                            13
C1orf112                         1                            65                        19                            29                        18                         0                            26
FGR                             35                          3946                       976                          4738                      4174                       156                          2688
         X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                           0                            17                        25                           25                       32
DPM1                            42                            58                        29                          110                       76
SCYL3                           15                            27                        15                           17                        4
C1orf112                         4                             3                         3                            3                        7
FGR                           1714                           827                       395                         6258                      152
22541 more rows ...

$unshrunk.coefficients
         (Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153  patientX154 patientX157 patientX158  patientX79    groupHSP
TSPAN6    -12.757132  -0.9887031 -19.8083301  -3.2566338  -1.5518658 -20.0868731  -0.8938202 -1.34010758 -1.65585639  -1.8337681 -20.08685760 -19.7897259  0.30453865  0.46826294  0.58431126
DPM1      -10.756455  -0.4179986  -1.7162842  -0.6813077  -0.5058401  -2.8818124  -0.7424711 -0.32148954 -0.58317586  -0.4485443  -0.84500206  -0.6955349 -0.73686737 -0.07995256  0.01737079
SCYL3     -12.353203   0.0223894   0.7107271  -0.9097191   0.3438188   0.5210835  -1.0357690  0.07946997 -0.02492036  -0.2269692 -17.21565672  -0.6398806  0.02113243 -0.87073217  0.29066454
C1orf112  -12.697894   0.6263001   0.7043160   0.6667196  -0.3004584 -16.7158447   0.6218703 -1.76895105  0.58483391  -0.3519180 -16.71583860  -0.1018623 -1.16087620 -0.61370289 -0.38583070
FGR        -8.000221   0.6059922  -0.9364748   0.6859240  -0.3316362  -1.8666510   0.1734921 -1.39908477 -0.02294654   0.3187617  -0.09810467   0.4605228 -0.58352979  0.46470992 -0.51534626
22541 more rows ...

$df.residual
[1] 11 11 11 11 11
22541 more elements ...

$design
                              (Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 patientX79 groupHSP
X108_Hip_non.sclerotic_pellet           1           0           0           0           0           0           0           0           0           0           0           0           0          0        0
X108_Hip_sclerotic_pellet               1           0           0           0           0           0           0           0           0           0           0           0           0          0        1
X125_Hip_non.sclerotic_pellet           1           1           0           0           0           0           0           0           0           0           0           0           0          0        0
X125_Hip_sclerotic_pellet               1           1           0           0           0           0           0           0           0           0           0           0           0          0        1
X126_Hip_non.sclerotic_pellet           1           0           1           0           0           0           0           0           0           0           0           0           0          0        0
21 more rows ...

$offset
         [,1]     [,2]    [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 13.89201 14.84671 15.9292 15.77668 13.86552 14.47325 14.13307 16.33213 16.40323 15.29499 14.31404 15.67059 15.70889 14.01081 14.02739 16.63058 15.17437 16.43352 16.30949 13.66353 15.65444 15.32218 15.48299 14.92266
       [,25]    [,26]
[1,] 15.6586 15.03913
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 26
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
22541 more rows ...

$dispersion
[1] 1.2941672 0.3067184 0.6271888 0.9164669 0.1527956
22541 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1] 1.079363 3.670427 2.294829 1.648604 8.148595
22541 more elements ...

$df.residual.zeros
[1]  9 11 11 11 11
22541 more elements ...

$df.prior
[1] 22.577519 22.577519 22.577519 22.577519  1.078782
22541 more elements ...

$var.post
[1] 1.063867 1.055797 1.393853 1.415116 3.083415
22541 more elements ...

$var.prior
[1] 1.3642386 1.1102524 1.3280847 1.3649516 0.5939256
22541 more elements ...

$samples
21 more rows ...

$genes
22541 more rows ...


$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.8259643

$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.9538669

$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 1.868611

$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.207767


$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$text
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.168457 2.168457

$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 0.8898118 0.5718562



$hip_pellet_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$hip_pellet_sclerotic_vs_non_sclerotic$boxplot_gg


$hip_sclerotic_vs_non_sclerotic
$hip_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"

$hip_sclerotic_vs_non_sclerotic$results
Coefficient:  groupsclerotic 

$hip_sclerotic_vs_non_sclerotic$colsums_samples

$hip_sclerotic_vs_non_sclerotic$normalized_matrix
                          X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet
TSPAN6                                        6.136374e+00                  3.657106e+00                 5.182608e+00              3.872889e+00                     4.959875e+00                  1.670471e+00
TNMD                                          1.022729e+00                  0.000000e+00                 1.295652e+00              0.000000e+00                     0.000000e+00                  0.000000e+00
DPM1                                          1.370457e+01                  1.645698e+01                 1.635761e+01              2.570190e+01                     1.289568e+01                  1.038078e+01
SCYL3                                         6.136374e+00                  9.142766e+00                 3.239130e-01              3.520808e-01                     1.842239e+00                  4.772773e+00
C1orf112                                      1.227275e+00                  6.399936e+00                 1.295652e+00              0.000000e+00                     3.542768e+00                  4.772773e+00
FGR                                           9.429562e+01                  2.194264e+02                 8.502717e+01              2.640606e+02                     1.424193e+02                  4.330098e+02
CFH                                           6.136374e+00                  5.485660e+00                 6.478260e+00              3.520808e-01                     1.417107e+00                  3.579580e-01
FUCA2                                         1.615912e+01                  2.742830e+00                 8.583695e+00              1.408323e+01                     1.615502e+01                  1.193193e+01
GCLC                                          4.009098e+01                  2.194264e+01                 4.372826e+01              2.429357e+01                     6.065219e+01                  8.304625e+01
NFYA                                          3.334097e+01                  3.565679e+01                 4.583369e+01              5.140380e+01                     3.812018e+01                  7.457458e+01
STPG1                                         1.206820e+01                  2.742830e+00                 1.133696e+01              4.224970e+00                     3.826189e+00                  5.727328e+00
NIPAL3                                        7.977286e+00                  9.142766e+00                 2.202608e+01              2.253317e+01                     1.842239e+01                  1.742062e+01
LAS1L                                         6.463648e+01                  5.759943e+01                 5.571304e+01              6.126206e+01                     6.306127e+01                  6.526767e+01
ENPP4                                         3.272733e+00                  7.314213e+00                 2.753261e+00              1.161867e+01                     8.502643e-01                  3.102302e+00
SEMA3F                                        5.727283e+01                  3.657106e+01                 5.004456e+01              4.224970e+01                     2.607477e+01                  1.909109e+00
ANKIB1                                        2.863641e+01                  8.228489e+00                 2.364565e+01              1.584364e+01                     2.961754e+01                  1.849450e+01
CYP51A1                                       1.043184e+01                  8.228489e+00                 1.603369e+01              1.197075e+01                     1.162028e+01                  5.965966e+00
KRIT1                                         1.084093e+01                  3.657106e+00                 9.393477e+00              3.168727e+00                     9.069486e+00                  1.706266e+01
RAD52                                         7.568195e+00                  1.097132e+01                 1.133696e+01              1.056242e+01                     1.417107e+01                  1.753994e+01
                          X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6                                    1.173139e+00              8.341759e-01                     0.000000e+00                  0.000000e+00                 7.419682e+00              0.000000e+00
TNMD                                      9.776156e-02              0.000000e+00                     4.302316e-01                  0.000000e+00                 3.709841e-01              0.000000e+00
DPM1                                      4.985839e+00              1.765672e+01                     1.118602e+01                  9.390996e-01                 7.048698e+00              6.134758e+00
SCYL3                                     1.955231e+00              5.283114e+00                     4.732548e+00                  1.314739e+01                 4.080825e+00              6.134758e+00
C1orf112                                  1.564185e+00              4.448938e+00                     0.000000e+00                  0.000000e+00                 0.000000e+00              8.179677e+00
FGR                                       5.664305e+02              4.671385e+02                     9.766257e+01                  1.380476e+02                 3.709841e+01              7.259463e+01
CFH                                       2.052993e+00              1.112234e+00                     1.936042e+00                  0.000000e+00                 0.000000e+00              3.067379e+00
FUCA2                                     1.965007e+01              8.619817e+00                     2.258716e+01                  2.817299e+00                 2.114609e+01              1.278075e+01
GCLC                                      5.738603e+01              6.687310e+01                     2.344762e+01                  1.033010e+01                 1.372641e+01              1.482566e+01
NFYA                                      4.985839e+01              4.768705e+01                     4.130223e+01                  2.347749e+01                 4.526006e+01              2.607272e+01
STPG1                                     4.790316e+00              6.256319e+00                     2.366274e+00                  4.695498e+00                 2.967873e+00              5.112298e-01
NIPAL3                                    1.300229e+01              1.362487e+01                     1.290695e+01                  3.192939e+01                 1.038755e+01              1.738181e+01
LAS1L                                     4.575241e+01              4.476744e+01                     4.173247e+01                  5.071138e+01                 5.193777e+01              4.447699e+01
ENPP4                                     1.564185e+00              4.448938e+00                     6.023242e+00                  0.000000e+00                 2.967873e+00              1.022460e+00
SEMA3F                                    1.564185e+01              1.404196e+01                     1.161625e+01                  3.850308e+01                 7.048698e+00              5.419036e+01
ANKIB1                                    2.248516e+01              1.515419e+01                     2.387785e+01                  2.441659e+01                 2.671086e+01              3.322994e+01
CYP51A1                                   1.094929e+01              5.422143e+00                     7.098821e+00                  7.512797e+00                 1.892019e+01              7.157217e+00
KRIT1                                     1.583737e+01              1.014914e+01                     1.075579e+01                  8.451896e+00                 1.780724e+01              6.645988e+00
RAD52                                     5.474647e+00              7.924671e+00                     8.174400e+00                  9.390996e-01                 1.409740e+01              1.278075e+01
                          X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet
TSPAN6                                        0.000000e+00                  0.000000e+00                 2.931600e+00              2.393611e-01                     6.483222e+00                  8.172430e-01
TNMD                                          0.000000e+00                  0.000000e+00                 3.664501e-01              0.000000e+00                     0.000000e+00                  1.485896e-01
DPM1                                          5.960540e+00                  5.030144e+00                 7.695451e+00              1.563826e+01                     1.166980e+01                  2.109973e+01
SCYL3                                         2.649129e+00                  0.000000e+00                 1.465800e+00              3.749991e+00                     5.834900e+00                  3.343267e+00
C1orf112                                      4.635975e+00                  1.006029e+01                 1.099350e+00              1.436167e+00                     0.000000e+00                  3.937625e+00
FGR                                           4.377685e+02                  7.106874e+02                 4.316782e+02              3.614353e+02                     2.022765e+02                  3.919052e+02
CFH                                           0.000000e+00                  7.185919e-01                 0.000000e+00              2.393611e-01                     0.000000e+00                  3.714741e-01
FUCA2                                         9.271951e+00                  6.467327e+00                 1.850573e+01              1.380316e+01                     2.398792e+01                  1.589909e+01
GCLC                                          5.364486e+01                  6.036172e+01                 6.138039e+01              3.742012e+01                     4.732752e+01                  6.887129e+01
NFYA                                          2.880928e+01                  4.167833e+01                 3.921016e+01              5.648922e+01                     2.528457e+01                  6.069886e+01
STPG1                                         4.635975e+00                  1.365325e+01                 0.000000e+00              2.154250e+00                     9.076511e+00                  2.303139e+00
NIPAL3                                        1.953733e+01                  1.437184e+01                 1.392510e+01              3.574459e+01                     1.750470e+01                  2.659754e+01
LAS1L                                         6.059882e+01                  5.964313e+01                 5.753266e+01              5.098392e+01                     3.436108e+01                  4.799445e+01
ENPP4                                         0.000000e+00                  1.437184e+00                 2.198700e+00              6.702111e+00                     1.491141e+01                  5.497816e+00
SEMA3F                                        9.934233e+00                  2.155776e+00                 1.612380e+01              7.978704e+00                     1.815302e+01                  4.011920e+00
ANKIB1                                        2.218645e+01                  7.904511e+00                 2.271990e+01              1.531911e+01                     2.009799e+01                  1.463608e+01
CYP51A1                                       6.953963e+00                  7.185919e+00                 8.061901e+00              7.579768e+00                     0.000000e+00                  1.151570e+01
KRIT1                                         1.092766e+01                  1.940198e+01                 1.502445e+01              9.654231e+00                     5.834900e+00                  1.641915e+01
RAD52                                         2.351102e+01                  6.467327e+00                 2.033798e+01              1.204784e+01                     9.724833e+00                  1.240723e+01
                          X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte
TSPAN6                                    2.181492e+00              6.746903e-01                     3.631162e+00                 2.791457e+00              0.000000e+00                     3.900121e+00
TNMD                                      2.726866e-01              0.000000e+00                     4.841549e-01                 0.000000e+00              0.000000e+00                     4.105390e-01
DPM1                                      2.208761e+01              4.048142e+00                     1.355634e+01                 1.500408e+01              1.199176e+00                     1.221354e+01
SCYL3                                     2.181492e+00              1.169463e+01                     1.040933e+01                 3.489321e-01              9.593405e+00                     3.592217e+00
C1orf112                                  2.454179e+00              2.248968e-01                     4.841549e-01                 2.093593e+00              0.000000e+00                     4.208025e+00
FGR                                       6.599015e+01              4.925239e+01                     1.101452e+01                 2.023806e+01              3.057898e+01                     1.529258e+02
CFH                                       1.636119e+00              7.646490e+00                     1.573503e+00                 8.723303e+00              4.197115e+00                     1.231617e+00
FUCA2                                     1.554313e+01              1.461829e+01                     1.476673e+01                 2.128486e+01              2.638186e+01                     2.288755e+01
GCLC                                      2.399642e+01              3.373451e+01                     3.812720e+01                 1.639981e+01              2.038599e+01                     6.404409e+01
NFYA                                      4.499328e+01              2.721251e+01                     3.473812e+01                 4.187186e+01              2.818063e+01                     5.193319e+01
STPG1                                     2.454179e+00              1.574277e+00                     1.391945e+01                 1.256156e+01              2.997939e+00                     4.823834e+00
NIPAL3                                    1.445239e+01              2.114030e+01                     2.251320e+01                 9.421168e+00              2.338392e+01                     2.442707e+01
LAS1L                                     3.190433e+01              3.733286e+01                     5.821963e+01                 5.233982e+01              2.578228e+01                     4.361977e+01
ENPP4                                     1.090746e+00              0.000000e+00                     4.357394e+00                 6.978643e-01              0.000000e+00                     4.926468e+00
SEMA3F                                    1.990612e+01              2.766230e+01                     3.122799e+01                 2.372739e+01              5.156455e+01                     2.093749e+01
ANKIB1                                    1.745194e+01              2.361416e+01                     4.006382e+01                 3.454428e+01              1.738805e+01                     2.483761e+01
CYP51A1                                   1.036209e+01              1.529298e+01                     6.051937e+00                 9.770100e+00              1.139217e+01                     6.979164e+00
KRIT1                                     7.362537e+00              4.273038e+00                     1.331426e+01                 7.676507e+00              2.997939e+00                     1.334252e+01
RAD52                                     1.608851e+01              7.421593e+00                     1.077245e+01                 6.629711e+00              4.796702e+00                     1.385569e+01
                          X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet
TSPAN6                                     1.082135e+00                 3.561243e+00              2.227513e+00                  0.000000e+00                 9.144607e+00              2.396549e+00
TNMD                                       0.000000e+00                 0.000000e+00              0.000000e+00                  0.000000e+00                 0.000000e+00              0.000000e+00
DPM1                                       8.193307e+00                 1.215012e+01              1.202857e+01                  2.111086e+01                 1.195833e+01              9.586196e+00
SCYL3                                      1.236726e+00                 3.491415e+00              2.376014e+00                  0.000000e+00                 3.798529e+00              1.198275e+01
C1orf112                                   5.565265e+00                 2.793132e+00              3.861023e+00                  0.000000e+00                 8.441176e-01              7.988497e-01
FGR                                        1.884461e+02                 2.284782e+02              3.578871e+02                  1.152978e+02                 2.870000e+01              2.795974e+01
CFH                                        1.082135e+00                 1.536223e+00              0.000000e+00                  0.000000e+00                 2.391666e+00              2.396549e+01
FUCA2                                      1.066676e+01                 1.249927e+01              1.826561e+01                  8.119561e+00                 1.547549e+01              2.396549e+01
GCLC                                       6.910204e+01                 8.058186e+01              7.395343e+01                  1.055543e+01                 2.884068e+01              2.636204e+01
NFYA                                       3.725636e+01                 5.753852e+01              6.192486e+01                  3.572607e+01                 2.870000e+01              6.470682e+01
STPG1                                      5.874446e+00                 3.631072e+00              2.079012e+00                  4.059780e+00                 2.813725e+00              6.390797e+00
NIPAL3                                     2.519828e+01                 2.045969e+01              2.524515e+01                  1.623912e+00                 9.848038e+00              2.636204e+01
LAS1L                                      4.313080e+01                 4.322372e+01              3.415520e+01                  4.628150e+01                 3.728186e+01              4.553443e+01
ENPP4                                      1.700498e+00                 4.259526e+00              3.118518e+00                  5.683693e+00                 7.034313e+00              3.195399e+00
SEMA3F                                     1.499530e+01                 2.164677e+01              8.613050e+00                  3.653802e+01                 1.927402e+01              2.875859e+01
ANKIB1                                     1.514989e+01                 2.842012e+01              1.989912e+01                  4.059780e+00                 2.813725e+01              3.115514e+01
CYP51A1                                    6.338219e+00                 8.239740e+00              8.316049e+00                  4.059780e+00                 8.722548e+00              1.118390e+01
KRIT1                                      8.811670e+00                 7.820770e+00              5.791534e+00                  1.786303e+01                 1.631961e+01              3.994248e+00
RAD52                                      1.020299e+01                 9.147508e+00              6.831040e+00                  7.307605e+00                 1.392794e+01              1.278159e+01
                          X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet
TSPAN6                                        9.764704e-02                  6.525487e-01                 1.352079e+00              7.610445e-01                     2.599881e+00                  3.608779e-01
TNMD                                          0.000000e+00                  0.000000e+00                 0.000000e+00              0.000000e+00                     1.575685e-01                  0.000000e+00
DPM1                                          1.122941e+01                  1.465268e+01                 6.995539e+00              8.878853e+00                     9.769249e+00                  1.551775e+01
SCYL3                                         2.538823e+00                  4.152582e+00                 5.231958e+00              5.580993e+00                     3.860429e+00                  3.753131e+00
C1orf112                                      1.855294e+00                  3.855969e+00                 3.233232e+00              4.819949e+00                     1.890822e+00                  2.093092e+00
FGR                                           3.861940e+02                  2.340870e+02                 3.816390e+02              2.475931e+02                     1.381876e+02                  3.419679e+02
CFH                                           0.000000e+00                  5.932261e-02                 5.290744e-01              1.775771e+00                     1.418117e+00                  1.515687e+00
FUCA2                                         1.552588e+01                  1.299165e+01                 1.975211e+01              1.192303e+01                     2.024756e+01                  1.436294e+01
GCLC                                          9.256939e+01                  1.060688e+02                 1.270954e+02              5.403416e+01                     6.940894e+01                  9.043601e+01
NFYA                                          6.796234e+01                  4.989031e+01                 5.913876e+01              4.414058e+01                     3.923457e+01                  5.110032e+01
STPG1                                         4.003529e+00                  6.110228e+00                 4.938027e+00              1.522089e+00                     7.563290e+00                  4.619238e+00
NIPAL3                                        3.583646e+01                  2.817824e+01                 3.409590e+01              3.526173e+01                     2.954410e+01                  3.031375e+01
LAS1L                                         5.204587e+01                  7.029729e+01                 6.554644e+01              4.388690e+01                     4.561609e+01                  5.903963e+01
ENPP4                                         4.101176e+00                  2.788162e+00                 6.172534e+00              5.073630e+00                     4.727056e+00                  1.660039e+00
SEMA3F                                        6.932940e+00                  3.855969e+00                 4.820455e+00              7.356764e+00                     2.237473e+01                  4.474886e+00
ANKIB1                                        1.093647e+01                  1.886459e+01                 2.322049e+01              1.141567e+01                     2.426555e+01                  1.667256e+01
CYP51A1                                       3.612940e+00                  6.644132e+00                 5.878604e+00              1.243039e+01                     1.024195e+01                  4.330535e+00
KRIT1                                         1.044823e+01                  1.500862e+01                 1.210992e+01              8.625171e+00                     7.169368e+00                  9.815880e+00
RAD52                                         1.093647e+01                  1.471201e+01                 8.523976e+00              7.864127e+00                     8.114780e+00                  1.891000e+01
                          X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte
TSPAN6                                    3.166526e+00              9.816047e-01                     3.477854e+00                 0.000000e+00              0.000000e+00                     4.128843e+00
TNMD                                      0.000000e+00              3.272016e-01                     0.000000e+00                 0.000000e+00              0.000000e+00                     6.162452e-02
DPM1                                      1.233278e+01              1.161566e+01                     7.321799e+00                 5.892579e+00              9.193218e+00                     9.859923e+00
SCYL3                                     4.499799e+00              4.090020e+00                     3.660899e+00                 4.910483e+00              0.000000e+00                     4.375341e+00
C1orf112                                  3.083196e+00              1.472407e+00                     1.647405e+00                 1.473145e+00              0.000000e+00                     4.128843e+00
FGR                                       1.044953e+02              3.414348e+02                     1.365515e+02                 1.301278e+02              1.792678e+02                     2.085374e+02
CFH                                       3.749833e+00              2.290411e+00                     7.321799e-01                 0.000000e+00              1.149152e+01                     4.128843e+00
FUCA2                                     1.416604e+01              1.112485e+01                     8.603114e+00                 1.031201e+01              1.034237e+01                     1.996634e+01
GCLC                                      5.008110e+01              6.912133e+01                     6.260138e+01                 6.874676e+01              1.493898e+01                     1.181342e+02
NFYA                                      4.074818e+01              4.180000e+01                     3.789031e+01                 5.156007e+01              3.217626e+01                     4.270579e+01
STPG1                                     4.749788e+00              4.008219e+00                     7.321799e-01                 4.910483e-01              0.000000e+00                     4.991586e+00
NIPAL3                                    1.974912e+01              2.339491e+01                     2.983633e+01                 3.191814e+01              5.630846e+01                     2.317082e+01
LAS1L                                     5.516421e+01              6.863053e+01                     5.564567e+01                 4.468539e+01              6.779998e+01                     5.003911e+01
ENPP4                                     4.999777e+00              1.227006e+00                     2.379585e+00                 0.000000e+00              0.000000e+00                     3.204475e+00
SEMA3F                                    2.641549e+01              4.090020e+00                     3.624290e+01                 1.129411e+01              2.872881e+01                     1.867223e+01
ANKIB1                                    2.274899e+01              2.085910e+01                     2.800588e+01                 1.571354e+01              2.298304e+00                     2.255457e+01
CYP51A1                                   9.416247e+00              9.407045e+00                     2.013495e+00                 1.964193e+00              9.193218e+00                     5.238084e+00
KRIT1                                     5.666414e+00              8.998043e+00                     9.884428e+00                 9.820965e+00              1.378983e+01                     1.041454e+01
RAD52                                     1.083285e+01              1.709628e+01                     7.504844e+00                 3.928386e+00              1.953559e+01                     1.281790e+01
                          X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte
TSPAN6                                     0.000000e+00                 1.655888e+00              0.000000e+00                     7.530164e+00                  3.168995e+00                 1.200208e+01
TNMD                                       0.000000e+00                 2.128999e+00              0.000000e+00                     0.000000e+00                  0.000000e+00                 0.000000e+00
DPM1                                       1.193856e+01                 1.324710e+01              9.195299e+00                     2.053681e+00                  1.081186e+01                 1.524588e+01
SCYL3                                      2.042121e+00                 7.333218e+00              3.284035e+00                     6.845604e+00                  5.033109e+00                 9.082654e+00
C1orf112                                   4.084243e+00                 7.096663e-01              8.757428e-01                     0.000000e+00                  5.592343e-01                 2.432854e+00
FGR                                        4.222479e+02                 1.627501e+02              3.752558e+02                     3.696626e+01                  1.541623e+02                 3.714157e+01
CFH                                        0.000000e+00                 0.000000e+00              1.751486e+00                     0.000000e+00                  3.914640e+00                 2.757234e+00
FUCA2                                      2.073539e+01                 1.324710e+01              1.729592e+01                     6.845604e-01                  1.025263e+01                 1.573245e+01
GCLC                                       6.566205e+01                 5.535397e+01              3.459184e+01                     6.571780e+01                  7.829281e+01                 4.119633e+01
NFYA                                       3.644401e+01                 4.778420e+01              4.991734e+01                     5.476483e+00                  4.194257e+01                 4.184509e+01
STPG1                                      3.298811e+00                 4.021442e+00              2.846164e+00                     0.000000e+00                  7.456458e+00                 1.362398e+01
NIPAL3                                     2.419128e+01                 1.182777e+01              1.773379e+01                     1.095297e+01                  1.994602e+01                 1.070456e+01
LAS1L                                      6.299159e+01                 4.139720e+01              3.700013e+01                     5.476483e+01                  3.318124e+01                 4.800832e+01
ENPP4                                      2.984639e+00                 8.515996e+00              3.284035e+00                     0.000000e+00                  1.491292e+00                 3.243805e-01
SEMA3F                                     2.356294e+00                 2.483832e+01              1.904741e+01                     6.297955e+01                  2.404708e+01                 3.697938e+01
ANKIB1                                     1.727949e+01                 2.602110e+01              8.976364e+00                     1.506033e+01                  1.845473e+01                 4.152071e+01
CYP51A1                                    1.068187e+01                 5.440775e+00              1.335508e+01                     1.232209e+01                  1.938679e+01                 2.351759e+01
KRIT1                                      7.854313e+00                 1.135466e+01              6.787007e+00                     8.899285e+00                  1.006622e+01                 1.265084e+01
RAD52                                      1.021061e+01                 4.257998e+00              7.005942e+00                     1.163753e+01                  1.118469e+01                 8.596084e+00
                          X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                                 8.158025e+00                 3.911500e+00             9.292487e+00
TNMD                                   0.000000e+00                 0.000000e+00             0.000000e+00
DPM1                                   9.463308e+00                 1.721060e+01             2.206966e+01
SCYL3                                  4.894815e+00                 2.659820e+00             1.161561e+00
C1orf112                               9.789629e-01                 4.693800e-01             2.032731e+00
FGR                                    1.288968e+02                 9.791268e+02             4.413931e+01
CFH                                    8.810666e+00                 6.258401e-01             8.711706e+00
FUCA2                                  1.435812e+01                 1.126512e+01             2.758707e+01
GCLC                                   2.741096e+01                 4.474756e+01             1.742341e+01
NFYA                                   3.589531e+01                 5.773375e+01             2.061771e+01
STPG1                                  3.589531e+00                 5.006720e+00             2.323122e+00
NIPAL3                                 5.873778e+00                 2.112210e+01             3.165253e+01
LAS1L                                  3.981116e+01                 5.382225e+01             3.716995e+01
ENPP4                                  2.284247e+00                 3.911500e+00             8.711706e-01
SEMA3F                                 3.361106e+01                 1.486370e+01             2.613512e+01
ANKIB1                                 2.251615e+01                 9.700521e+00             1.626185e+01
CYP51A1                                8.810666e+00                 1.048282e+01             6.388585e+00
KRIT1                                  5.873778e+00                 5.632561e+00             6.678975e+00
RAD52                                  8.484345e+00                 1.157804e+01             2.265044e+01
 [ reached getOption("max.print") -- omitted 24217 rows ]

$hip_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept)   batchX125   batchX126  batchX129  batchX143  batchX145  batchX146  batchX150  batchX152   batchX153  batchX154  batchX157  batchX158    batchX79 groupsclerotic
TSPAN6     -12.33137 -0.74791232 -0.96087551 -1.7390972 -0.6658406 -0.7372784 -0.5685940 -0.2252624 -1.8982352 -0.99280749 -1.1574732 -1.1134907  0.4550240  0.28920498    0.167194394
TNMD       -14.39331 -2.66463827 -0.93490153 -1.7132316 -1.5560487 -1.0402376 -1.5376495 -3.5476169 -3.4609786 -1.52235863 -3.4588215 -0.2141448 -3.4894572 -3.45333113    0.222145494
DPM1       -10.93500 -0.45117712 -0.99602745 -0.7205204 -0.1943065 -0.5728656 -0.4794864 -0.2438546 -0.5402957 -0.37982433 -0.8957897 -0.4879768 -0.6287768  0.08400982    0.023396235
SCYL3      -12.48798 -0.07986258  0.60149968 -0.5715893  0.4258639  0.5923505 -0.3307001  0.3235805  0.1511724  0.07684324 -0.1945072  0.1237574  0.5433720 -0.65359876   -0.001410283
C1orf112   -13.08304  0.58465196  0.06123562  0.7103485 -0.1249699 -0.7750417  0.7191525 -1.1240017  0.5552093  0.08095515 -0.5150790  0.2001690 -0.5815277 -0.45293591   -0.085067274
24231 more rows ...

$fitted.values
         X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte
TSPAN6                          21.444640                     4.7976851                    32.125403                 14.777625                       14.5958907                    17.3349471                   25.0959029
TNMD                             2.492638                     0.5576635                     4.503811                  2.071745                        0.1430746                     0.1699239                    0.2967056
DPM1                            87.040545                    19.4730769                   112.536102                 51.766397                       79.9648461                    94.9710029                  118.6620317
SCYL3                           18.339522                     4.1029950                    23.128962                 10.639279                       24.4356250                    29.0212002                   35.3699136
C1orf112                        10.059231                     2.2504935                    11.684098                  5.374663                       26.1809913                    31.0941010                   34.9026889
         X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet
TSPAN6                  17.6467435                        7.7403366                      1.773048                    5.3237113                 3.8632572                        2.2832984                     1.0521882
TNMD                     0.2086352                        0.8989678                      0.205923                    0.7457443                 0.5411642                        0.2291998                     0.1056197
DPM1                    83.4398524                       30.5153217                      6.990023                   18.1139454                13.1447455                       26.1279485                    12.0402655
SCYL3                   24.8711431                       31.9039416                      7.308109                   18.4729952                13.4052971                        6.3753773                     2.9378975
C1orf112                24.5426036                       10.1721073                      2.330084                    5.4245805                 3.9364549                       12.7151000                     5.8593648
         X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte
TSPAN6                      4.8947285                 11.240382                        3.4627718                      30.21734                    9.7653693                11.8404772                        17.271022
TNMD                        0.5926131                  1.360892                        0.1468117                       1.28113                    0.4993633                 0.6054764                         1.480462
DPM1                       48.3405609                111.010525                       22.6068552                     197.27522                   55.0231443                66.7153759                        82.880739
SCYL3                      11.5056229                 26.421813                        8.8763948                      77.45848                   21.0736487                25.5517276                        56.187173
C1orf112                   21.1342228                 48.533180                        2.8002893                      24.43629                    6.1230567                 7.4241855                         7.740460
         X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6                      7.1062269                 4.1354926                       24.1238844                    16.0161584                    42.057926                19.7765419                  4.302635e+00
TNMD                        0.7346991                 0.4275606                        0.9968963                     0.6618523                     2.096243                 0.9856987                  2.156279e-09
DPM1                       29.4316828                17.1278664                      107.3229064                    71.2530634                   161.485484                75.9339496                  1.717690e+01
SCYL3                      19.4624063                11.3262126                       26.2129474                    17.4031143                    38.472889                18.0907801                  6.395888e+00
C1orf112                    2.4693826                 1.4370655                       41.3821792                    27.4741631                    55.938980                26.3037124                  8.076395e-01
         X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte
TSPAN6                   2.945459e+01              5.187279e+00                     6.571185e+00                  1.081640e+01                 1.294691e+01              3.000210e+00                        20.479626
TNMD                     1.780387e-08              3.135459e-09                     1.953570e-08                  3.215643e-08                 4.642401e-08              1.075791e-08                         1.227007
DPM1                     1.014854e+02              1.787271e+01                     1.061389e+02                  1.747082e+02                 1.804835e+02              4.182374e+01                       154.490713
SCYL3                    3.686020e+01              6.491488e+00                     4.473069e+01                  7.362824e+01                 7.419359e+01              1.719301e+01                        51.451613
C1orf112                 4.286834e+00              7.549588e-01                     3.687878e+01                  6.070373e+01                 5.633777e+01              1.305525e+01                        28.351493
         X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte
TSPAN6                       22.354821                    22.966762                 23.396117                     7.482972e+00                 3.308608e+00              1.413813e+00                        23.204272
TNMD                          1.339357                     1.659648                  1.690674                     1.026689e-08                 5.475217e-09              2.339634e-09                         6.215055
DPM1                        168.636488                   149.527327                152.322686                     3.964879e+01                 1.513010e+01              6.465294e+00                       177.230711
SCYL3                        56.162725                    48.575252                 49.483349                     1.686236e+01                 6.276652e+00              2.682098e+00                        68.952551
C1orf112                     30.947467                    24.652119                 25.112981                     6.680843e+00                 2.290357e+00              9.787003e-01                        40.901361
         X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet
TSPAN6                        9.102974                     7.170116                  7.747160                     1.010851e+01                  3.712158e+01                 5.060715e+01              2.515311e+01
TNMD                          2.438149                     2.316297                  2.502711                     2.746090e-09                  1.008449e-08                 1.658176e-08              8.241577e-09
DPM1                         69.527136                    47.264785                 51.068609                     1.385587e+01                  5.088302e+01                 5.986855e+01              2.975627e+01
SCYL3                        27.049902                    17.936881                 19.380423                     9.458360e+00                  3.473402e+01                 3.986381e+01              1.981338e+01
C1orf112                     16.045495                     9.799335                 10.587976                     1.668663e+00                  6.127847e+00                 6.477299e+00              3.219391e+00
         X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                   3.744719e+01             2.393196e+01
TNMD                     1.236318e-08             9.529723e-09
DPM1                     1.237747e+02             6.827023e+01
SCYL3                    1.241698e+01             6.680569e+00
C1orf112                 8.311105e+00             4.118304e+00
24231 more rows ...

$deviance
[1] 54.11683 14.05643 24.70806 34.13150 36.82026
24231 more elements ...

$iter
[1] 11 18  5  6 10
24231 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
24231 more elements ...

$method
[1] "levenberg"

$counts
         X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte
TSPAN6                                 30                             4                           32                        11                               35                            14                           12
TNMD                                    5                             0                            8                         0                                0                             0                            1
DPM1                                   67                            18                          101                        73                               91                            87                           51
SCYL3                                  30                            10                            2                         1                               13                            40                           20
C1orf112                                6                             7                            8                         0                               25                            40                           16
         X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet
TSPAN6                           6                                0                             0                           20                         0                                0                             0
TNMD                             0                                2                             0                            1                         0                                0                             0
DPM1                           127                               52                             1                           19                        12                               18                             7
SCYL3                           38                               22                            14                           11                        12                                8                             0
C1orf112                        32                                0                             0                            0                        16                               14                            14
         X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte
TSPAN6                             16                         3                               10                            11                            8                         3                               30
TNMD                                2                         0                                0                             2                            1                         0                                4
DPM1                               42                       196                               18                           284                           81                        18                              112
SCYL3                               8                        47                                9                            45                            8                        52                               86
C1orf112                            6                        18                                0                            53                            9                         1                                4
         X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6                              8                         0                               38                             7                           51                        15                             0
TNMD                                0                         0                                4                             0                            0                         0                             0
DPM1                               43                         2                              119                            53                          174                        81                            26
SCYL3                               1                        16                               35                             8                           50                        16                             0
C1orf112                            6                         0                               41                            36                           40                        26                             0
         X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte
TSPAN6                             65                         3                                1                            11                           23                         3                               33
TNMD                                0                         0                                0                             0                            0                         0                                2
DPM1                               85                        12                              115                           247                          119                        35                              124
SCYL3                              27                        15                               26                            70                           89                        22                               49
C1orf112                            6                         1                               19                            65                           55                        19                               24
         X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte
TSPAN6                               5                           38                        12                               19                            0                         0                               67
TNMD                                 0                            0                         4                                0                            0                         0                                1
DPM1                               215                          148                       142                               40                           12                         8                              160
SCYL3                               52                           54                        50                               20                           10                         0                               71
C1orf112                            29                           37                        18                                9                            3                         0                               67
         X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet
TSPAN6                               0                            7                         0                               11                            17                           74                        25
TNMD                                 0                            9                         0                                0                             0                            0                         0
DPM1                                76                           56                        42                                3                            58                           94                        29
SCYL3                               13                           31                        15                               10                            27                           56                        15
C1orf112                            26                            3                         4                                0                             3                           15                         3
         X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                             25                       32
TNMD                                0                        0
DPM1                              110                       76
SCYL3                              17                        4
C1orf112                            3                        7
24231 more rows ...

$unshrunk.coefficients
         (Intercept)   batchX125   batchX126  batchX129  batchX143  batchX145  batchX146   batchX150   batchX152   batchX153   batchX154  batchX157   batchX158     batchX79 groupsclerotic
TSPAN6     -12.33700 -0.75173887 -0.96864502 -1.7581010 -0.6698095 -0.7411260 -0.5718876  -0.2275929  -1.9222132 -1.00012282  -1.1639048 -1.1208705   0.4558880   0.28946537    0.170708215
TNMD       -14.48913 -3.22473507 -0.96946511 -1.9047503 -1.6783501 -1.0456686 -1.6060655 -19.4895694 -19.4037965 -1.66284233 -19.4187433 -0.2860992 -19.4184444 -19.38987639    0.358118203
DPM1       -10.93610 -0.45179108 -0.99776059 -0.7216158 -0.1945250 -0.5736527 -0.4801472  -0.2441544  -0.5410582 -0.38031868  -0.8973737 -0.4886538  -0.6296805   0.08409741    0.023435910
SCYL3      -12.49342 -0.08002045  0.60405571 -0.5748625  0.4279329  0.5949487 -0.3324202   0.3252512   0.1521688  0.07750480  -0.1950344  0.1246281   0.5458254  -0.65798477   -0.001436905
C1orf112   -13.09398  0.58953874  0.06154321  0.7160522 -0.1251721 -0.7867109  0.7247443  -1.1434759   0.5597130  0.08211036  -0.5203066  0.2029405  -0.5884830  -0.45888961   -0.083726112
24231 more rows ...

$df.residual
[1] 36 36 36 36 36
24231 more elements ...

$design
                                 (Intercept) batchX125 batchX126 batchX129 batchX143 batchX145 batchX146 batchX150 batchX152 batchX153 batchX154 batchX157 batchX158 batchX79 groupsclerotic
X108_Hip_non.sclerotic_adipocyte           1         0         0         0         0         0         0         0         0         0         0         0         0        0              0
X108_Hip_non.sclerotic_pellet              1         0         0         0         0         0         0         0         0         0         0         0         0        0              0
X108_Hip_sclerotic_adipocyte               1         0         0         0         0         0         0         0         0         0         0         0         0        0              1
X108_Hip_sclerotic_pellet                  1         0         0         0         0         0         0         0         0         0         0         0         0        0              1
X125_Hip_non.sclerotic_adipocyte           1         1         0         0         0         0         0         0         0         0         0         0         0        0              0
46 more rows ...

$offset
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]   [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 15.40247 13.90513 15.63594 14.85941 15.76948 15.94146 16.14073 15.78858 15.35209 13.87834 14.80711 14.48645 14.92072 14.14597 15.51255 16.3439 14.24888 16.41522 15.11494 15.30762 15.92716 14.86839 14.32702 16.09209
        [,25]    [,26]    [,27]    [,28]    [,29]    [,30]    [,31]    [,32]    [,33]    [,34]    [,35]    [,36]    [,37]    [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]   [,48]
[1,] 15.68248 16.47723 15.72268 14.02382 15.77673 14.04009 16.14191 16.64028 16.64936 15.18719 16.35655 16.44416 16.30046 16.31898 15.51353 14.52672 13.67649 16.60221 15.66647 15.25708 15.33449 14.19449 15.49531 15.6345
        [,49]    [,50]    [,51]
[1,] 14.93538 15.67047 15.05204
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 51
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
24231 more rows ...

$dispersion
[1] 1.0143221 5.8528321 0.3673950 0.7130623 1.1664206
24231 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  1.623798 -1.089619  3.571136  2.221472  1.400589
24231 more elements ...

$df.residual.zeros
[1] 36 25 36 36 36
24231 more elements ...

$df.prior
[1] 17.58321 17.58321 17.58321 17.58321 17.58321
24231 more elements ...

$var.post
[1] 1.3991035 0.6415641 0.7757505 1.0198302 1.0738508
24231 more elements ...

$var.prior
[1] 1.1858827 0.7543233 0.9588205 1.1666969 1.1784033
24231 more elements ...

$samples
46 more rows ...

$genes
24231 more rows ...


$hip_sclerotic_vs_non_sclerotic$mds_plot
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.459672

$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.9221995

$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 1.509402

$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.714582


$hip_sclerotic_vs_non_sclerotic$mds_plot$text
$hip_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 1.812565 1.812565

$hip_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 1.407183 1.099783



$hip_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$hip_sclerotic_vs_non_sclerotic$boxplot_gg


$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$results
Coefficient:  groupsclerotic 

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$colsums_samples

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$normalized_matrix
                          X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet
TSPAN6                                       2.656555e-01                9.205954e+00                    5.481659e+00                6.903021e+00                    7.019917e+00                3.517982e+00
DPM1                                         1.567368e+01                1.380893e+01                    1.837968e+01                6.903021e+00                    1.432063e+01                1.348560e+01
SCYL3                                        5.401662e+00                3.287841e+00                    2.257154e+00                6.275473e+00                    2.246373e+00                3.517982e+00
C1orf112                                     6.287181e+00                0.000000e+00                    2.902055e+00                0.000000e+00                    5.615933e-01                0.000000e+00
FGR                                          1.183230e+03                2.048325e+02                    1.222088e+02                7.028530e+01                    1.555614e+02                8.384523e+01
CFH                                          7.969666e-01                3.616625e+00                    1.612253e+00                2.510189e+00                    6.551922e-01                4.104312e+00
FUCA2                                        1.222015e+01                1.906948e+01                    6.126560e+00                1.736214e+01                    1.057667e+01                2.052156e+01
GCLC                                         5.118296e+01                1.972704e+01                    1.708988e+01                1.045912e+01                    2.695648e+01                5.276973e+00
NFYA                                         6.030380e+01                3.517989e+01                    3.998387e+01                3.179573e+01                    3.266601e+01                3.928413e+01
STPG1                                        2.302348e+00                6.246897e+00                    3.546956e+00                8.367298e-01                    4.867142e+00                1.583092e+01
NIPAL3                                       1.859589e+01                1.052109e+01                    5.159209e+00                1.234176e+01                    1.656700e+01                2.873018e+01
LAS1L                                        5.268834e+01                3.781017e+01                    7.448607e+01                2.238252e+01                    4.839062e+01                2.345321e+01
ENPP4                                        1.372554e+01                4.602977e+00                    3.224505e+00                3.346919e+00                    7.955905e+00                3.517982e+00
SEMA3F                                       1.505381e+00                2.268610e+01                    7.771058e+01                5.229561e+01                    5.728252e+01                3.224817e+01
ANKIB1                                       8.058217e+00                1.380893e+01                    1.289802e+01                1.066830e+01                    1.656700e+01                9.967615e+00
CYP51A1                                      6.818492e+00                8.219602e+00                    1.322047e+01                8.785663e+00                    6.926318e+00                1.055395e+01
KRIT1                                        1.142319e+01                9.534738e+00                    1.708988e+01                1.652541e+01                    1.647340e+01                9.381285e+00
                          X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet
TSPAN6                                       5.071507e-01                    13.99923                    2.672109e+00                6.451039e+00                    8.433707e-01                    8.063157e+00
DPM1                                         2.015924e+01                    29.55393                    2.240461e+01                1.319531e+01                    1.766118e+01                    1.075088e+01
SCYL3                                        2.028603e+00                    10.88829                    3.905390e+00                5.571352e+00                    1.835572e+00                    2.150175e+00
C1orf112                                     2.916117e+00                     0.00000                    3.802617e+00                1.172916e+00                    3.720753e+00                    0.000000e+00
FGR                                          4.218226e+02                    88.66179                    3.603236e+02                4.896925e+01                    6.631871e+02                    1.311607e+02
CFH                                          7.607260e-01                     6.22188                    4.110937e-01                4.691665e+00                    2.976603e-01                    7.525613e+00
FUCA2                                        1.242519e+01                     3.11094                    1.891031e+01                4.984894e+00                    9.922009e+00                    6.450526e+00
GCLC                                         6.402778e+01                    29.55393                    4.994788e+01                7.330726e+00                    1.044291e+02                    1.505123e+01
NFYA                                         3.867024e+01                    27.99846                    3.915667e+01                2.697707e+01                    5.328119e+01                    5.912982e+00
STPG1                                        3.930418e+00                    13.99923                    4.624804e+00                1.759374e+00                    4.861784e+00                    2.150175e+00
NIPAL3                                       1.825743e+01                    18.66564                    1.870476e+01                2.140572e+01                    1.954636e+01                    8.600701e+00
LAS1L                                        4.057206e+01                    40.44222                    4.881737e+01                4.105207e+01                    6.022659e+01                    3.171508e+01
ENPP4                                        6.085808e+00                     4.66641                    8.119100e+00                3.518749e+00                    3.125433e+00                    2.150175e+00
SEMA3F                                       3.030225e+01                    20.22111                    9.660701e+00                3.577394e+01                    1.031889e+01                    3.171508e+01
ANKIB1                                       1.052338e+01                    12.44376                    7.399686e+00                2.404478e+01                    8.532927e+00                    6.450526e+00
CYP51A1                                      7.860836e+00                     0.00000                    5.241444e+00                9.676559e+00                    8.136047e+00                    8.063157e+00
KRIT1                                        1.026980e+01                     3.11094                    1.387441e+01                1.143593e+01                    1.830611e+01                    1.451368e+01
                          X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet
TSPAN6                                       9.589878                    1.223865e+01                4.798319e+01                    8.027498e+00                3.773157e+00                    2.969127e+01
DPM1                                         0.000000                    1.398703e+01                4.798319e+00                    1.245646e+01                1.207410e+01                    1.370366e+01
SCYL3                                        1.369983                    6.702120e+00                6.397759e+00                    0.000000e+00                7.546314e-01                    4.567888e+00
C1orf112                                     0.000000                    1.165586e+00                0.000000e+00                    8.304308e-01                0.000000e+00                    1.141972e+00
FGR                                         87.678883                    5.303417e+01                3.198880e+01                    1.309313e+02                8.678262e+01                    5.595663e+01
CFH                                         27.399651                    2.913965e+00                1.599440e+01                    1.107241e+00                1.056484e+01                    7.993804e+00
FUCA2                                       10.959860                    1.544402e+01                0.000000e+00                    6.920257e+00                5.282420e+00                    2.854930e+01
GCLC                                        31.509599                    1.398703e+01                1.279552e+01                    1.494775e+01                1.433800e+01                    2.055549e+01
NFYA                                        31.509599                    4.283529e+01                3.358824e+01                    1.688543e+01                1.131947e+01                    4.339493e+01
STPG1                                        5.479930                    1.107307e+01                6.397759e+00                    8.304308e+00                2.263894e+00                    0.000000e+00
NIPAL3                                      30.139616                    8.159103e+00                2.559104e+01                    2.186801e+01                3.018526e+01                    1.941352e+01
LAS1L                                       42.469459                    2.826546e+01                4.158544e+01                    4.235197e+01                2.490284e+01                    2.169747e+01
ENPP4                                        0.000000                    8.159103e+00                4.798319e+00                    5.536205e-01                1.509263e+00                    0.000000e+00
SEMA3F                                      28.769634                    4.516646e+01                1.759384e+01                    4.179835e+01                3.546768e+01                    5.595663e+01
ANKIB1                                      19.179756                    9.907482e+00                1.439496e+01                    1.522456e+01                9.810209e+00                    4.567888e+00
CYP51A1                                     39.729494                    6.410724e+00                0.000000e+00                    1.134922e+01                1.131947e+01                    6.851832e+00
KRIT1                                       15.069808                    8.741896e+00                0.000000e+00                    1.079560e+01                7.546314e-01                    1.141972e+01
                          X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet
TSPAN6                                   1.447908e+01                    5.168783e+00                6.664913e+00                    4.256301e+00                3.230201e+00                    1.941976e+01
DPM1                                     1.990873e+01                    1.174723e+01                9.873945e+00                    1.895989e+01                9.788489e+00                    8.091569e+00
SCYL3                                    9.049423e-01                    2.036187e+00                3.702729e+00                    5.417111e+00                3.915395e+00                    9.709882e+00
C1orf112                                 9.049423e-01                    4.698894e-01                2.468486e-01                    4.256301e+00                5.873093e-01                    0.000000e+00
FGR                                      7.601516e+01                    5.818797e+01                3.529935e+01                    3.405041e+01                4.404820e+01                    8.334316e+01
CFH                                      9.049423e-01                    3.054281e+00                2.962184e+00                    6.964857e+00                5.187899e+00                    8.091569e-01
FUCA2                                    9.049423e+00                    1.613287e+01                2.937499e+01                    1.470359e+01                9.886374e+00                    2.912965e+01
GCLC                                     1.719390e+01                    2.388604e+01                1.925419e+01                    2.553781e+01                2.711411e+01                    2.912965e+01
NFYA                                     1.809885e+01                    2.764516e+01                3.233717e+01                    3.211573e+01                2.564584e+01                    2.184723e+01
STPG1                                    6.334596e+00                    3.994060e+00                9.873945e-01                    5.804047e+00                2.447122e+00                    1.861061e+01
NIPAL3                                   4.524712e+00                    1.237375e+01                8.639702e+00                    4.643238e+00                1.076734e+01                    1.537398e+01
LAS1L                                    5.248666e+01                    3.367541e+01                2.517856e+01                    2.515087e+01                3.494490e+01                    3.803037e+01
ENPP4                                    9.049423e-01                    4.777209e+00                4.196427e+00                    1.238197e+01                1.859813e+00                    0.000000e+00
SEMA3F                                   1.990873e+01                    4.174184e+01                5.060397e+01                    4.565850e+01                7.243482e+01                    4.207616e+01
ANKIB1                                   9.049423e+00                    1.683770e+01                1.086134e+01                    1.509052e+01                1.174619e+01                    1.780145e+01
CYP51A1                                  1.719390e+01                    1.550635e+01                1.950104e+01                    1.934682e+01                1.311657e+01                    1.861061e+01
KRIT1                                    3.619769e+00                    1.010262e+01                1.061449e+01                    1.238197e+01                8.613870e+00                    4.854941e+00
                          X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                                   1.558993e+01                    1.461662e+00                    1.322539e+01                5.796559e+00                   9.592093e+00               7.089689e+00
DPM1                                     9.977557e+00                    1.218051e+01                    1.098725e+01                9.274495e+00                   2.599148e+01               3.038438e+01
SCYL3                                    2.494389e+00                    1.948882e+00                    3.255481e+00                4.869110e+00                   1.856534e+00               1.012813e+00
C1orf112                                 1.247195e+00                    0.000000e+00                    1.220805e+00                0.000000e+00                   0.000000e+00               0.000000e+00
FGR                                      5.820242e+01                    6.577478e+01                    4.272819e+01                4.335826e+01                   1.191276e+02               9.317878e+01
CFH                                      2.078658e-01                    9.257191e+00                    4.883221e+00                3.014211e+00                   1.237689e+01               1.012813e+01
FUCA2                                    2.328097e+01                    4.872206e+00                    1.261499e+01                2.434555e+01                   1.856534e+01               0.000000e+00
GCLC                                     1.746073e+01                    7.795529e+00                    1.668434e+01                1.808526e+01                   1.299574e+01               1.417938e+01
NFYA                                     2.452816e+01                    1.510384e+01                    2.767159e+01                1.112939e+01                   1.639939e+01               3.443563e+01
STPG1                                    7.483168e+00                    2.923323e+00                    5.086689e+00                8.115183e+00                   0.000000e+00               9.115315e+00
NIPAL3                                   1.891579e+01                    3.020767e+01                    1.403926e+01                1.507105e+01                   1.454285e+01               1.519219e+01
LAS1L                                    2.723042e+01                    2.728435e+01                    4.008311e+01                3.338818e+01                   3.620242e+01               2.025626e+01
ENPP4                                    4.988779e+00                    5.359426e+00                    1.831208e+00                2.086761e+00                   3.403646e+00               2.025626e+00
SEMA3F                                   3.970236e+01                    2.923323e+01                    4.049004e+01                3.918474e+01                   3.867780e+01               2.329469e+01
ANKIB1                                   1.455060e+01                    1.023163e+01                    1.281846e+01                8.347045e+00                   8.044982e+00               6.076877e+00
CYP51A1                                  1.600566e+01                    1.315496e+01                    1.098725e+01                2.388182e+01                   2.104072e+01               1.823063e+01
KRIT1                                    1.288768e+01                    5.846647e+00                    8.952573e+00                1.205684e+01                   1.547112e+00               2.126907e+01
                          X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet
TSPAN6                                     3.464896e+00              3.732628e+00                  1.733443e+00              8.625461e-01                      0.000000              0.000000e+00
DPM1                                       1.559203e+01              2.477108e+01                  1.077211e+01              1.825723e+01                      0.889069              5.913613e+00
SCYL3                                      8.662239e+00              3.393298e-01                  4.952693e+00              5.462792e+00                     12.446965              5.913613e+00
C1orf112                                   6.063567e+00              0.000000e+00                  4.952693e+00              4.600246e+00                      0.000000              7.884818e+00
FGR                                        2.078937e+02              2.544974e+02                  4.493331e+02              4.830258e+02                    130.693137              6.997776e+01
CFH                                        5.197343e+00              3.393298e-01                  3.714520e-01              1.150061e+00                      0.000000              2.956807e+00
FUCA2                                      2.598672e+00              1.357319e+01                  1.238173e+01              8.912976e+00                      2.667207              1.232003e+01
GCLC                                       2.078937e+01              2.341376e+01                  8.617687e+01              6.914745e+01                      9.779759              1.429123e+01
NFYA                                       3.378273e+01              4.954216e+01                  7.738583e+01              4.930889e+01                     22.226724              2.513286e+01
STPG1                                      2.598672e+00              4.071958e+00                  5.943232e+00              6.469096e+00                      4.445345              4.928011e-01
NIPAL3                                     8.662239e+00              2.171711e+01                  1.807733e+01              1.408825e+01                     30.228345              1.675524e+01
LAS1L                                      5.457211e+01              5.904339e+01                  6.772808e+01              4.628997e+01                     48.009724              4.287370e+01
ENPP4                                      6.929791e+00              1.119789e+01                  3.219251e+00              4.600246e+00                      0.000000              9.856022e-01
SEMA3F                                     3.464896e+01              4.071958e+01                  1.981077e+00              1.451953e+01                     36.451827              5.223692e+01
ANKIB1                                     7.796015e+00              1.526984e+01                  1.919169e+01              1.566959e+01                     23.115793              3.203207e+01
CYP51A1                                    7.796015e+00              1.153721e+01                  6.190867e+00              5.606550e+00                      7.112552              6.899215e+00
KRIT1                                      3.464896e+00              3.053969e+00                  1.770588e+01              1.049431e+01                      8.001621              6.406414e+00
                          X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet
TSPAN6                                     0.000000e+00              2.364098e-01                  8.568633e-01              6.429349e-01                  0.000000                  1.092095e+00              2.266115e+00
DPM1                                       5.055205e+00              1.544544e+01                  2.212265e+01              3.857610e+00                  1.153388                  8.268723e+00              1.223702e+01
SCYL3                                      0.000000e+00              3.703754e+00                  3.505350e+00              1.114421e+01                  9.227104                  1.248109e+00              2.417189e+00
C1orf112                                   1.011041e+01              1.418459e+00                  4.128523e+00              2.143116e-01                  0.000000                  5.616491e+00              3.927933e+00
FGR                                        7.142283e+02              3.569788e+02                  4.109049e+02              4.693425e+01                 29.411396                  1.901806e+02              3.640891e+02
CFH                                        7.221722e-01              2.364098e-01                  3.894833e-01              7.286596e+00                  4.036858                  1.092095e+00              0.000000e+00
FUCA2                                      6.499549e+00              1.363297e+01                  1.666989e+01              1.393026e+01                 25.374537                  1.076494e+01              1.858214e+01
GCLC                                       6.066246e+01              3.695874e+01                  7.221021e+01              3.214675e+01                 19.607597                  6.973809e+01              7.523502e+01
NFYA                                       4.188598e+01              5.579272e+01                  6.364157e+01              2.593171e+01                 27.104619                  3.759929e+01              6.299800e+01
STPG1                                      1.372127e+01              2.127688e+00                  2.414797e+00              1.500181e+00                  2.883470                  5.928518e+00              2.115041e+00
NIPAL3                                     1.444344e+01              3.530387e+01                  2.788701e+01              2.014529e+01                 22.491067                  2.543022e+01              2.568264e+01
LAS1L                                      5.994029e+01              5.035529e+01                  5.032125e+01              3.557573e+01                 24.797843                  4.352780e+01              3.474710e+01
ENPP4                                      1.444344e+00              6.619475e+00                  5.764353e+00              0.000000e+00                  0.000000                  1.716150e+00              3.172561e+00
SEMA3F                                     2.166516e+00              7.880328e+00                  4.206420e+00              2.636033e+01                 49.595687                  1.513332e+01              8.762311e+00
ANKIB1                                     7.943894e+00              1.513023e+01                  1.534564e+01              2.250272e+01                 16.724127                  1.528934e+01              2.024396e+01
CYP51A1                                    7.221722e+00              7.486311e+00                  1.207398e+01              1.457319e+01                 10.957187                  6.396559e+00              8.460163e+00
KRIT1                                      1.949865e+01              9.535196e+00                  1.721516e+01              4.071921e+00                  2.883470                  8.892777e+00              5.891899e+00
                          X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet
TSPAN6                                     0.000000e+00              2.318259e+00                  6.800126e-01              7.810061e-01                  3.793702e-01              1.011839e+00              0.000000e+00
DPM1                                       1.997198e+01              9.273036e+00                  1.526937e+01              9.111738e+00                  1.631292e+01              1.197343e+01              8.721136e+00
SCYL3                                      0.000000e+00              1.159129e+01                  4.327353e+00              5.727378e+00                  3.945450e+00              4.215997e+00              0.000000e+00
C1orf112                                   0.000000e+00              7.727530e-01                  4.018256e+00              4.946372e+00                  2.200347e+00              1.517759e+00              0.000000e+00
FGR                                        1.090777e+02              2.704635e+01                  2.439391e+02              2.540873e+02                  3.594912e+02              3.519514e+02              1.700621e+02
CFH                                        0.000000e+00              2.318259e+01                  6.181933e-02              1.822348e+00                  1.593355e+00              2.360958e+00              1.090142e+01
FUCA2                                      7.681531e+00              2.318259e+01                  1.353843e+01              1.223576e+01                  1.509893e+01              1.146751e+01              9.811278e+00
GCLC                                       9.985990e+00              2.550085e+01                  1.105330e+02              5.545143e+01                  9.507018e+01              7.125035e+01              1.417185e+01
NFYA                                       3.379874e+01              6.259299e+01                  5.199006e+01              4.529835e+01                  5.371882e+01              4.308749e+01              3.052398e+01
STPG1                                      3.840765e+00              6.182024e+00                  6.367391e+00              1.562012e+00                  4.855939e+00              4.131677e+00              0.000000e+00
NIPAL3                                     1.536306e+00              2.550085e+01                  2.936418e+01              3.618662e+01                  3.186710e+01              2.411550e+01              5.341696e+01
LAS1L                                      4.378473e+01              4.404692e+01                  7.325591e+01              4.503802e+01                  6.206497e+01              7.074443e+01              6.431838e+01
ENPP4                                      5.377072e+00              3.091012e+00                  2.905509e+00              5.206707e+00                  1.745103e+00              1.264799e+00              0.000000e+00
SEMA3F                                     3.456689e+01              2.781911e+01                  4.018256e+00              7.549726e+00                  4.704191e+00              4.215997e+00              2.725355e+01
ANKIB1                                     3.840765e+00              3.013737e+01                  1.965855e+01              1.171509e+01                  1.752690e+01              2.150159e+01              2.180284e+00
CYP51A1                                    3.840765e+00              1.081854e+01                  6.923765e+00              1.275643e+01                  4.552443e+00              9.696794e+00              8.721136e+00
KRIT1                                      1.689937e+01              3.863765e+00                  1.564029e+01              8.851402e+00                  1.031887e+01              9.275194e+00              1.308170e+01
                          X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                                     0.000000e+00              0.000000e+00                  3.186183e+00              7.952143e+00                 3.971011e+00             9.013019e+00
DPM1                                       1.187537e+01              9.108305e+00                  1.087051e+01              9.224486e+00                 1.747245e+01             2.140592e+01
SCYL3                                      2.031314e+00              3.252966e+00                  5.060408e+00              4.771286e+00                 2.700288e+00             1.126627e+00
C1orf112                                   4.062628e+00              8.674576e-01                  5.622676e-01              9.542572e-01                 4.765213e-01             1.971598e+00
FGR                                        4.200132e+02              3.717056e+02                  1.549984e+02              1.256439e+02                 9.940235e+02             4.281184e+01
CFH                                        0.000000e+00              1.734915e+00                  3.935873e+00              8.588315e+00                 6.353618e-01             8.449706e+00
FUCA2                                      2.062565e+01              1.713229e+01                  1.030824e+01              1.399577e+01                 1.143651e+01             2.675740e+01
GCLC                                       6.531456e+01              3.426458e+01                  7.871746e+01              2.671920e+01                 4.542837e+01             1.689941e+01
NFYA                                       3.625114e+01              4.944509e+01                  4.217007e+01              3.498943e+01                 5.861212e+01             1.999764e+01
STPG1                                      3.281354e+00              2.819237e+00                  7.496901e+00              3.498943e+00                 5.082894e+00             2.253255e+00
NIPAL3                                     2.406326e+01              1.756602e+01                  2.005421e+01              5.725543e+00                 2.144346e+01             3.070060e+01
LAS1L                                      6.265823e+01              3.665008e+01                  3.336121e+01              3.880646e+01                 5.464111e+01             3.605208e+01
ENPP4                                      2.968844e+00              3.252966e+00                  1.499380e+00              2.226600e+00                 3.971011e+00             8.449706e-01
SEMA3F                                     2.343824e+00              1.886720e+01                  2.417750e+01              3.276283e+01                 1.508984e+01             2.534912e+01
ANKIB1                                     1.718804e+01              8.891441e+00                  1.855483e+01              2.194792e+01                 9.848107e+00             1.577278e+01
CYP51A1                                    1.062534e+01              1.322873e+01                  1.949194e+01              8.588315e+00                 1.064231e+01             6.196451e+00
KRIT1                                      7.812746e+00              6.722797e+00                  1.012082e+01              5.725543e+00                 5.718256e+00             6.478108e+00
 [ reached getOption("max.print") -- omitted 23225 rows ]

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) patientX104  patientX108 patientX109  patientX125 patientX126 patientX128 patientX129 patientX130 patientX143  patientX144 patientX145 patientX146 patientX148 patientX149 patientX150 patientX151
TSPAN6    -12.642272   0.5325985 -0.080613894   0.3955203 -1.010286258  -5.1385721  0.41050782  -3.0212127   0.3072877  -1.5486785  0.099471185  -5.2559682  -0.8666274 -1.31514557   0.8290270 -1.27287292   1.9373396
DPM1      -11.065634   0.1626920  0.340278139  -0.6954884  0.002112572  -1.3507482 -0.05833726  -0.2856111   0.5133298  -0.1520034  0.180426458  -2.4673866  -0.3478365  0.12286875  -0.9047451 -0.02337654  -0.3983677
SCYL3     -12.384791  -0.6058934 -0.008575266   0.2612114  0.148928373   0.7284506 -0.46629456  -0.7756743   0.2193185   0.4476305  0.043073847   0.6454715  -0.9044528 -0.81019575  -0.8630459  0.19450174   0.3930328
C1orf112  -12.576950  -0.1647928 -0.118073809  -4.0442767  0.864822252   1.0335640 -2.01090884   0.6713779  -0.4881926  -0.3208318 -0.005272773  -4.0442767   0.8033260  0.08188315  -4.7628170 -1.53519923  -1.2890593
FGR        -7.167284  -1.8422965 -0.859499288  -1.8374300 -0.176669788  -1.8079688 -1.63001536  -0.1426857  -0.9710598  -1.1383440 -1.237558652  -2.7081297  -0.6248754 -0.15113247  -1.6940841 -2.28031304  -2.6534987
         patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX79 patientX99 groupsclerotic
TSPAN6    -1.6188126 -1.74496016  -5.2559682   0.5207178   1.8055717 -5.05918744  0.29963178   0.4198674 -0.01460916   1.5325354  -0.7771552   0.9810127  0.4603485  0.8248522      0.3667191
DPM1      -0.1954187 -0.04664149  -0.4624305  -0.1836762   0.1477250 -0.34266764 -0.38321850  -0.3102676 -0.04850762  -0.4652037  -0.2480437  -0.3754778  0.2838924  0.6497761     -0.1189107
SCYL3      0.1055391 -0.09251174  -5.2953181  -2.8061170  -0.4869201 -0.53994659  0.09863435  -0.4689260  0.04409532   0.3059762  -0.7510566  -0.1091942 -0.7979389 -1.0422844      0.1485874
C1orf112   0.8492516 -0.13561507  -4.0442767  -1.6920664  -0.7388067 -0.07624703 -0.92270464  -1.8196648 -0.18345592  -0.7184476  -4.9545718  -1.5351756 -0.3041042 -4.7929662     -0.9102951
FGR       -0.8088230 -0.45966983  -0.9540318  -1.6990193  -2.1062524 -0.36677364 -1.41670610  -2.5550757 -2.62653394  -2.1190526  -2.4616200  -2.5691132 -0.3652631 -1.7045656     -0.5578874
23237 more rows ...

$fitted.values
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6                          36.02512                   14.099079                              17                 3.30000e+01                       51.753060                  12.0050187                        34.25763
DPM1                           176.35681                   42.162972                              57                 3.30000e+01                      157.376731                  22.3008306                       205.93898
SCYL3                           46.93124                   14.700769                               7                 3.00000e+01                       27.744714                   5.1510976                        40.79670
C1orf112                        38.62770                    4.054426                               9                 5.00819e-08                        4.647315                   0.2891173                        16.54826
FGR                           8711.29982                 1342.868580                             379                 3.36000e+02                     1614.501215                 147.5130535                      2303.82450
         X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6                     4.0576176                        34.39318                   17.516388                              17                    1.369676e+01                7.809351e+00                       76.535012
DPM1                      14.9006807                       182.04472                   56.637497                             356                    1.173077e+01                4.085803e+00                       35.957357
SCYL3                      3.8675111                        42.20258                   17.202992                              37                    3.237621e+00                1.477461e+00                       21.161335
C1orf112                   0.5256678                        33.43625                    4.567042                              75                    2.775474e-08                4.244041e-09                        3.179583
FGR                      107.4802068                      2177.14435                  436.741783                           13368                    2.636735e+02                5.921462e+01                      186.280247
         X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6                    20.2616623                      19.5462473                  10.4185945                       17.168527                  31.4822684                       62.344617                  28.7416089
DPM1                       5.8150893                      46.9346042                  15.2824369                       15.856293                  17.7618563                      146.128865                  41.1530316
SCYL3                      4.4838462                       0.8185068                   0.3491892                        2.228389                   3.2705196                       33.068597                  12.2017072
C1orf112                   0.2257513                       2.1970448                   0.3140725                        1.430976                   0.7037373                        6.737386                   0.8330072
FGR                       19.4243722                     509.5118019                 106.9708043                       82.182090                  59.3574763                      764.842192                 138.8830413
         X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6                          8.156527                    46.85196                       18.421162                  104.199392                     3.00000e+00                        42.20003                   53.811626
DPM1                           38.444059                   134.89797                       12.109176                   41.842389                     2.50000e+01                        52.68636                   41.040747
SCYL3                          11.224337                    51.60311                        6.985233                   31.624365                     4.00000e+00                        18.28978                   18.666567
C1orf112                        7.378633                    11.36694                        2.084298                    3.161937                     2.15032e-08                         3.49239                    1.194349
FGR                           144.122905                   326.07745                      114.507115                  255.120828                     1.35000e+02                       290.28610                  145.799112
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet
TSPAN6                     2.371241e+01               1.052681e+01                      3.406774                 12.637171                      9.319524                  11.66387                  1.096997e-08
DPM1                       9.673412e+01               2.623339e+01                     25.349363                 57.441703                    126.398809                  96.63747                  4.529885e+00
SCYL3                      4.690892e+00               1.666745e+00                      4.757625                 14.125033                     38.967553                  39.03415                  9.711817e+00
C1orf112                   4.826867e-08               5.746872e-09                      3.501855                  3.483773                     67.312927                  22.59397                  1.120330e+01
FGR                        4.532910e+02               7.926169e+01                    377.025562                550.861738                   5221.426945                2573.96901                  1.422560e+02
         X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet
TSPAN6                2.875861e-08                     0.1936674                  2.579001                      8.535129                  4.507976               2.08324e-08                      8.543531
DPM1                  7.254426e+00                    16.2454380                132.153918                    172.153560                 55.544525               2.00000e+00                     70.644278
SCYL3                 2.037771e+01                     2.6326581                 28.059641                     83.549056                 35.318790               1.60000e+01                     10.688047
C1orf112              7.876868e+00                     9.3748227                 33.481367                     31.790611                  4.503142               1.81663e-08                     50.117850
FGR                   1.468920e+02                   926.1487316               4857.814376                   3172.066535                659.901477               5.10000e+01                   2646.963079
         X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet
TSPAN6                    12.82058                     1.1471255                 1.6569770                      9.995259                  3.448924                      7.140241                  9.336288
DPM1                      64.75913                    19.8591620                17.5234723                    207.699866                 43.780377                    196.427235                156.897772
SCYL3                     12.83694                     6.5684809                 7.5938708                     74.710715                 20.633134                     49.886991                 52.208521
C1orf112                  20.17010                     0.9299504                 0.3602555                    132.928000                 12.301307                     39.942490                 14.006890
FGR                     1564.52842                   102.6470558                58.4005993                   5557.576808                755.336231                   6420.423698               3306.665933
         X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                1.102062e-08                  6.385374e-08              6.685444e-08                     23.061782                 19.745535                     31.98273                26.209261
DPM1                  8.000000e+00                  7.089915e+01              4.534596e+01                     56.754769                 29.684661                    130.64919                65.403295
SCYL3                 1.546687e-07                  1.542958e+01              1.292976e+01                     24.477278                 16.773816                     11.70449                 7.676873
C1orf112              9.610306e-09                  2.042272e+01              5.734593e+00                      7.248624                  1.664473                     16.19771                 3.559902
FGR                   1.560000e+02                  3.421125e+03              1.410841e+03                    998.043476                336.581899                   3370.32390              1087.867783
23237 more rows ...

$deviance
[1] 21.91207 20.40764 23.04180 26.64643 56.79511
23237 more elements ...

$iter
[1] 20  6 17 19 10
23237 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
23237 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6                                 3                          28                              17                          33                              75                           6                               4
DPM1                                 177                          42                              57                          33                             153                          23                             159
SCYL3                                 61                          10                               7                          30                              24                           6                              16
C1orf112                              71                           0                               9                           0                               6                           0                              23
FGR                                13362                         623                             379                         336                            1662                         143                            3327
         X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6                             9                              26                          22                              17                              15                           7                              42
DPM1                              19                             218                          45                             356                              20                           0                              48
SCYL3                              7                              38                          19                              37                               4                           1                              23
C1orf112                           0                              37                           4                              75                               0                           0                               4
FGR                               57                            3506                         167                           13368                             244                          64                             182
         X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6                            30                              29                           5                              26                          16                              66                          27
DPM1                               3                              45                          16                              12                          22                             150                          40
SCYL3                              4                               0                           1                               4                           1                              26                          15
C1orf112                           0                               3                           0                               1                           1                               6                           1
FGR                               20                             473                         115                              49                          84                             743                         143
         X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6                                11                          33                              24                          75                               3                              65                          25
DPM1                                  49                         100                              10                          48                              25                              54                          40
SCYL3                                 14                          40                              12                          12                               4                              16                          21
C1orf112                              11                           6                               0                           6                               0                               6                           0
FGR                                   88                         450                             103                         280                             135                             210                         187
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet
TSPAN6                               31                          7                             4                        11                            14                         6                             0
DPM1                                 84                         30                            18                        73                            87                       127                             1
SCYL3                                 6                          1                            10                         1                            40                        38                            14
C1orf112                              0                          0                             7                         0                            40                        32                             0
FGR                                 385                         92                           240                       750                          3629                      3360                           147
         X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet
TSPAN6                           0                             0                         3                            11                         3                         0                             7
DPM1                            12                             7                       196                           284                        18                         2                            53
SCYL3                           12                             0                        47                            45                        52                        16                             8
C1orf112                        16                            14                        18                            53                         1                         0                            36
FGR                            142                           989                      4530                          5275                       219                        51                          1219
         X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet
TSPAN6                          15                             0                         3                            11                         3                             5                        12
DPM1                            81                            26                        12                           247                        35                           215                       142
SCYL3                           16                             0                        15                            70                        22                            52                        50
C1orf112                        26                             0                         1                            65                        19                            29                        18
FGR                           2410                           142                        35                          3946                       976                          4738                      4174
         X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6                           0                             0                         0                            17                        25                           25                       32
DPM1                             8                            76                        42                            58                        29                          110                       76
SCYL3                            0                            13                        15                            27                        15                           17                        4
C1orf112                         0                            26                         4                             3                         3                            3                        7
FGR                            156                          2688                      1714                           827                       395                         6258                      152
23237 more rows ...

$unshrunk.coefficients
         (Intercept) patientX104  patientX108 patientX109  patientX125 patientX126 patientX128 patientX129 patientX130 patientX143  patientX144 patientX145 patientX146 patientX148 patientX149 patientX150 patientX151
TSPAN6    -12.655461   0.5413584 -0.077895439   0.3982037 -1.016885724 -19.6057337  0.41769739  -3.1271540   0.3086184  -1.5682311  0.102580332 -19.7709554  -0.8726869 -1.33039802   0.8363645  -1.2865564   1.9446286
DPM1      -11.067168   0.1629036  0.340799622  -0.6972292  0.002152043  -1.3552261 -0.05843641  -0.2860217   0.5139964  -0.1523274  0.180681739  -2.4864845  -0.3484969  0.12302663  -0.9068720  -0.0234429  -0.3990787
SCYL3     -12.390994  -0.6104118 -0.008379744   0.2611032  0.149264946   0.7312464 -0.47020793  -0.7820142   0.2188432   0.4485453  0.042736356   0.6465996  -0.9132023 -0.81716055  -0.8704227   0.1939999   0.3945889
C1orf112  -12.585708  -0.1643834 -0.120121656 -18.6616096  0.890601912   1.0688257 -2.06224966   0.6827334  -0.4887630  -0.3230037  0.004609488 -18.6615959   0.8267629  0.08412363 -19.2504069  -1.5661927  -1.3061229
FGR        -7.167301  -1.8424785 -0.859508034  -1.8376465 -0.176631052  -1.8081614 -1.63016460  -0.1426660  -0.9711248  -1.1384428 -1.237668322  -2.7088270  -0.6248528 -0.15115207  -1.6942428  -2.2806789  -2.6540272
         patientX152 patientX153 patientX154 patientX155 patientX156  patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX79  patientX99 groupsclerotic
TSPAN6    -1.6414777 -1.77298345 -19.7709452   0.5283110   1.8157850 -19.58298645  0.30373767   0.4256105 -0.01072564   1.5416882  -0.7804755   0.9901228  0.4652917   0.8329009      0.3737060
DPM1      -0.1957872 -0.04673070  -0.4634388  -0.1840099   0.1479809  -0.34335011 -0.38399218  -0.3108707 -0.04863269  -0.4661411  -0.2485047  -0.3762343  0.2843186   0.6505760     -0.1191538
SCYL3      0.1055679 -0.09343686 -17.1712184  -2.9092130  -0.4904809  -0.54449673  0.09883904  -0.4729498  0.04407312   0.3075194  -0.7572605  -0.1104230 -0.8043993  -1.0519419      0.1510293
C1orf112   0.8764660 -0.12104247 -18.6615768  -1.7271123  -0.7386892  -0.06942111 -0.92338063  -1.8691480 -0.18070880  -0.7071329 -19.6039048  -1.5714649 -0.2847878 -19.2493337     -0.9423475
FGR       -0.8088309 -0.45965040  -0.9540453  -1.6991791  -2.1065152  -0.36675086 -1.41680207  -2.5555571 -2.62703745  -2.1193347  -2.4619727  -2.5695909 -0.3653001  -1.7047230     -0.5579999
23237 more rows ...

$df.residual
[1] 24 24 24 24 24
23237 more elements ...

$design
                                (Intercept) patientX104 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149
X102_tibia_non.sclerotic_pellet           1           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X102_tibia_sclerotic_pellet               1           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X104_tibia_non.sclerotic_pellet           1           1           0           0           0           0           0           0           0           0           0           0           0           0           0
X109_tibia_sclerotic_pellet               1           0           0           1           0           0           0           0           0           0           0           0           0           0           0
X128_tibia_non.sclerotic_pellet           1           0           0           0           0           0           1           0           0           0           0           0           0           0           0
                                patientX150 patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX79 patientX99
X102_tibia_non.sclerotic_pellet           0           0           0           0           0           0           0           0           0           0           0           0           0           0          0          0
X102_tibia_sclerotic_pellet               0           0           0           0           0           0           0           0           0           0           0           0           0           0          0          0
X104_tibia_non.sclerotic_pellet           0           0           0           0           0           0           0           0           0           0           0           0           0           0          0          0
X109_tibia_sclerotic_pellet               0           0           0           0           0           0           0           0           0           0           0           0           0           0          0          0
X128_tibia_non.sclerotic_pellet           0           0           0           0           0           0           0           0           0           0           0           0           0           0          0          0
                                groupsclerotic
X102_tibia_non.sclerotic_pellet              0
X102_tibia_sclerotic_pellet                  1
X104_tibia_non.sclerotic_pellet              0
X109_tibia_sclerotic_pellet                  1
X128_tibia_non.sclerotic_pellet              0
51 more rows ...

$offset
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 16.23968 14.92786 14.94732 15.38006 16.18425 14.34938 15.88075 13.37373 16.09074 15.04231 16.81907 14.43626 13.50071 15.04858 13.34586 15.09993 14.09704 13.68275 13.91539 16.36253 15.21449 14.76501 16.13947 14.02727
        [,25]    [,26]    [,27]    [,28]    [,29]    [,30]    [,31]    [,32]    [,33]    [,34]    [,35]    [,36]  [,37]    [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]    [,45]    [,46]   [,47]    [,48]
[1,] 15.38637 14.53455 15.40776 15.27712 14.98856 13.80278 13.95912 14.89629 15.90446 15.75514 13.93309 14.52316 14.141 16.35631 16.36788 15.35583 14.36595 15.67332 15.70549 14.07928 14.07331 16.59905 15.1613 16.39419
        [,49]   [,50]    [,51]    [,52]   [,53]    [,54]    [,55]    [,56]
[1,] 16.28865 13.7292 15.67178 15.34399 15.4899 14.96094 15.65537 15.08258
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 56
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23237 more rows ...

$dispersion
[1] 0.5439410 0.2957987 0.6792627 1.1165685 0.1538170
23237 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1] 2.527269 3.779531 2.131560 1.253292 7.756163
23237 more elements ...

$df.residual.zeros
[1] 22 24 24 22 24
23237 more elements ...

$df.prior
[1] 27.5638438 27.5638438 27.5638438 27.5638438  0.6333009
23237 more elements ...

$var.post
[1] 1.1742461 0.9813726 1.1688355 1.2968748 2.3196803
23237 more elements ...

$var.prior
[1] 1.3165100 1.0954825 1.3506044 1.3652549 0.5467717
23237 more elements ...

$samples
51 more rows ...

$genes
23237 more rows ...


$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.404493

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.7783497

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.113643

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.193974


$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.405346 2.405346

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 0.9345237 0.6750738



$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$boxplot_gg


$tibia_adipocytes_sclerotic_vs_non_sclerotic
$tibia_adipocytes_sclerotic_vs_non_sclerotic$name
[1] "TSA-vs-TNSA"

$tibia_adipocytes_sclerotic_vs_non_sclerotic$results
Coefficient:  groupTSA 

$tibia_adipocytes_sclerotic_vs_non_sclerotic$colsums_samples

$tibia_adipocytes_sclerotic_vs_non_sclerotic$normalized_matrix
                          X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte
TSPAN6                                      6.076363e+00                       4.597051e+00                       1.833306e+01                   4.549568e+00                       9.936451e+00
TNMD                                        0.000000e+00                       0.000000e+00                       7.051177e+00                   1.516523e+00                       9.243210e-01
DPM1                                        9.789696e+00                       1.264189e+01                       4.230706e+00                   9.604643e+00                       1.617562e+01
SCYL3                                       8.776969e+00                       9.960276e+00                       9.871647e+00                   3.033045e+00                       2.310803e+00
C1orf112                                    0.000000e+00                       0.000000e+00                       0.000000e+00                   0.000000e+00                       2.310803e-01
FGR                                         3.915878e+01                       1.394439e+02                       2.256377e+01                   6.622148e+01                       3.951472e+01
CFH                                         1.350303e+00                       4.213963e+00                       1.410235e+00                   6.571598e+00                       4.159445e+00
FUCA2                                       2.633091e+01                       1.264189e+01                       4.230706e+00                   1.314320e+01                       1.178509e+01
GCLC                                        2.565575e+01                       2.796539e+01                       5.993500e+01                   9.099135e+00                       3.327556e+01
NFYA                                        1.755394e+01                       5.401534e+01                       3.384565e+01                   5.307829e+01                       2.033506e+01
STPG1                                       1.080242e+01                       3.830875e-01                       7.051177e-01                   5.560583e+00                       2.772963e+00
NIPAL3                                      8.776969e+00                       4.213963e+00                       1.621771e+01                   1.314320e+01                       3.235124e+00
LAS1L                                       3.071939e+01                       8.849322e+01                       3.455077e+01                   4.195712e+01                       4.690929e+01
ENPP4                                       0.000000e+00                       2.298525e+00                       7.051177e-01                   5.055075e-01                       6.239167e+00
SEMA3F                                      4.050909e+01                       8.849322e+01                       4.865312e+01                   3.336350e+01                       1.525130e+01
ANKIB1                                      1.350303e+01                       1.225880e+01                       1.269212e+01                   1.465972e+01                       1.386482e+01
CYP51A1                                     1.654121e+01                       6.895576e+00                       4.935824e+00                   1.162667e+01                       8.781050e+00
KRIT1                                       6.076363e+00                       1.187571e+01                       1.057677e+01                   1.263769e+01                       9.705371e+00
RAD52                                       1.350303e+01                       3.064700e+00                       1.833306e+01                   0.000000e+00                       7.625648e+00
MYH16                                       0.000000e+00                       1.915438e+00                       0.000000e+00                   0.000000e+00                       6.932408e-01
BAD                                         6.211393e+01                       3.141318e+01                       4.371730e+01                   6.419945e+01                       6.955516e+01
LAP3                                        2.869394e+01                       4.673668e+01                       2.608935e+01                   3.488002e+01                       3.812824e+01
CD99                                        2.400163e+02                       1.647276e+02                       2.221121e+02                   2.471932e+02                       2.645869e+02
HS3ST1                                      1.451576e+01                       2.451760e+01                       9.166530e+00                   9.604643e+00                       1.086077e+01
AOC1                                        0.000000e+00                       5.746313e+00                       1.410235e+00                   0.000000e+00                       2.310803e-01
WNT16                                       1.012727e+00                       1.532350e+00                       1.410235e+00                   0.000000e+00                       6.932408e-01
HECW1                                       2.363030e+00                       1.532350e+00                       4.935824e+00                   8.088120e+00                       2.541883e+00
MAD1L1                                      1.012727e+01                       6.129401e+00                       3.525588e+00                   1.314320e+01                       5.545926e+00
LASP1                                       2.970666e+02                       1.831158e+02                       2.178814e+02                   2.153462e+02                       3.438474e+02
SNX11                                       1.181515e+01                       7.278663e+00                       1.621771e+01                   3.538553e+00                       5.777006e+00
TMEM176A                                    2.329272e+01                       3.332862e+01                       9.871647e+00                   4.448466e+01                       2.703639e+01
                          X109_tibia_sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte
TSPAN6                                      1.025967e+01                       7.166957e+00                   4.700622e+00                       7.881550e+00                       3.006245
TNMD                                        0.000000e+00                       0.000000e+00                   0.000000e+00                       0.000000e+00                       0.000000
DPM1                                        1.413555e+01                       1.522978e+01                   5.640747e+00                       1.069639e+01                      13.027061
SCYL3                                       2.963905e+00                       1.791739e+00                   4.700622e+00                       2.251871e+00                       0.000000
C1orf112                                    5.015839e+00                       0.000000e+00                   0.000000e+00                       5.629678e-01                       0.000000
FGR                                         8.321732e+01                       3.762652e+01                   3.290435e+01                       2.277205e+02                     200.416325
CFH                                         5.243831e+00                       1.791739e+00                   0.000000e+00                       1.125936e+00                       4.008327
FUCA2                                       1.778343e+01                       2.015707e+01                   1.598212e+01                       1.125936e+01                      12.024980
GCLC                                        3.579485e+01                       2.687609e+01                   3.666485e+01                       3.771885e+01                      26.054122
NFYA                                        1.846741e+01                       1.657359e+01                   5.452722e+01                       2.758542e+01                      17.035388
STPG1                                       6.383795e+00                       1.791739e+00                   2.820373e+00                       7.037098e+00                       0.000000
NIPAL3                                      8.207736e+00                       1.254217e+01                   8.461120e+00                       1.801497e+01                       4.008327
LAS1L                                       4.901842e+01                       3.538685e+01                   3.290435e+01                       2.955581e+01                      11.022898
ENPP4                                       1.823941e+00                       2.239674e+00                   3.760498e+00                       1.463716e+01                       4.008327
SEMA3F                                      2.576317e+01                       2.015707e+01                   2.068274e+01                       4.250407e+01                      15.031224
ANKIB1                                      1.003168e+01                       1.433391e+01                   3.196423e+01                       1.238529e+01                      16.033306
CYP51A1                                     1.732744e+01                       2.239674e+01                   1.222162e+01                       8.163034e+00                       3.006245
KRIT1                                       9.347699e+00                       1.881326e+01                   9.401244e+00                       1.013342e+01                       7.014571
RAD52                                       9.575692e+00                       1.612565e+01                   1.880249e+00                       9.007486e+00                       7.014571
MYH16                                       1.367956e+00                       0.000000e+00                   2.820373e+00                       5.629678e-01                       0.000000
BAD                                         5.608620e+01                       7.256544e+01                   4.230560e+01                       2.420762e+01                      31.064530
LAP3                                        3.898675e+01                       2.060500e+01                   4.794635e+01                       4.053368e+01                      28.058286
CD99                                        2.991264e+02                       3.171378e+02                   2.209292e+02                       1.531273e+02                     256.532897
HS3ST1                                      1.413555e+01                       8.958696e+00                   0.000000e+00                       1.773349e+01                       8.016653
AOC1                                        1.139963e+00                       0.000000e+00                   0.000000e+00                       1.970387e+00                       0.000000
WNT16                                       0.000000e+00                       8.958696e-01                   0.000000e+00                       2.814839e-01                       0.000000
HECW1                                       6.383795e+00                       8.958696e+00                   0.000000e+00                       5.629678e-01                       0.000000
MAD1L1                                      5.699817e+00                       5.375218e+00                   2.820373e+00                       1.435568e+01                       7.014571
LASP1                                       3.374291e+02                       3.973182e+02                   3.854510e+02                       3.445363e+02                     224.466284
SNX11                                       8.435729e+00                       1.478185e+01                   9.401244e+00                       5.066711e+00                      14.029143
TMEM176A                                    6.064605e+01                       2.777196e+01                   2.444324e+01                       2.280020e+01                      40.083265
                          X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte
TSPAN6                                          4.702029e+00                   7.378439e+00                       5.467025e+00                   1.025351e+01                       1.271424e+01
TNMD                                            7.233891e-02                   0.000000e+00                       4.970022e-01                   0.000000e+00                       2.801442e+00
DPM1                                            1.258697e+01                   1.249574e+01                       1.673241e+01                   2.343658e+01                       1.422271e+01
SCYL3                                           3.616946e+00                   3.689220e+00                       2.982013e+00                   2.929573e+00                       2.585946e+00
C1orf112                                        1.157423e+00                   1.666099e+00                       3.147681e+00                   0.000000e+00                       0.000000e+00
FGR                                             2.311228e+02                   1.122237e+02                       2.489981e+02                   4.599430e+02                       5.258091e+01
CFH                                             1.808473e+00                   2.618156e+00                       3.313348e-01                   0.000000e+00                       5.602884e+00
FUCA2                                           1.548053e+01                   1.630397e+01                       1.606974e+01                   4.394360e+00                       1.702415e+01
GCLC                                            4.694795e+01                   3.046581e+01                       7.372200e+01                   1.230421e+02                       3.447929e+01
NFYA                                            3.125041e+01                   2.725262e+01                       4.323920e+01                   5.859146e+01                       3.124685e+01
STPG1                                           7.523247e+00                   1.904113e+00                       9.111708e+00                   8.788719e+00                       5.171893e+00
NIPAL3                                          1.540819e+01                   6.664397e+00                       1.491007e+01                   5.859146e+00                       8.835317e+00
LAS1L                                           3.624180e+01                   3.510709e+01                       3.710950e+01                   2.197180e+01                       3.469478e+01
ENPP4                                           2.748879e+00                   3.451205e+00                       4.638688e+00                   4.394360e+00                       1.228325e+01
SEMA3F                                          2.539096e+01                   1.463787e+01                       4.837489e+01                   1.757744e+01                       2.736793e+01
ANKIB1                                          1.215294e+01                   1.547092e+01                       1.673241e+01                   0.000000e+00                       1.357622e+01
CYP51A1                                         9.765753e+00                   1.142468e+01                       1.474440e+01                   1.464787e+00                       1.142126e+01
KRIT1                                           1.454012e+01                   1.106766e+01                       6.792364e+00                   0.000000e+00                       6.680362e+00
RAD52                                           5.570096e+00                   4.522269e+00                       7.786369e+00                   2.929573e+00                       3.232433e+00
MYH16                                           0.000000e+00                   2.380142e-01                       8.283371e-01                   0.000000e+00                       0.000000e+00
BAD                                             4.123318e+01                   4.974496e+01                       4.688388e+01                   1.318308e+01                       5.236541e+01
LAP3                                            3.559075e+01                   3.332198e+01                       3.677817e+01                   2.197180e+01                       4.159064e+01
CD99                                            1.673922e+02                   1.988608e+02                       1.353503e+02                   1.274364e+02                       2.646285e+02
HS3ST1                                          1.063382e+01                   1.392383e+01                       9.111708e+00                   1.025351e+01                       7.757839e+00
AOC1                                            5.714774e+00                   2.380142e-01                       4.970022e+00                   0.000000e+00                       8.188830e+00
WNT16                                           1.012745e+00                   4.760283e-01                       6.626697e-01                   0.000000e+00                       8.619821e-01
HECW1                                           1.663795e+00                   4.998298e+00                       1.656674e+00                   0.000000e+00                       9.050812e+00
MAD1L1                                          9.187042e+00                   1.487589e+01                       8.614706e+00                   0.000000e+00                       7.326848e+00
LASP1                                           3.673370e+02                   3.554742e+02                       3.134428e+02                   2.021405e+02                       3.366040e+02
SNX11                                           1.859110e+01                   1.273376e+01                       1.590407e+01                   1.171829e+01                       1.099027e+01
TMEM176A                                        5.324144e+01                   6.723900e+01                       4.439887e+01                   5.859146e+00                       3.663424e+01
                          X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte
TSPAN6                                      1.135028e+01                       1.810273e+00                   0.000000e+00                       5.145781e+00                   7.277910e+00
TNMD                                        0.000000e+00                       0.000000e+00                   0.000000e+00                       0.000000e+00                   0.000000e+00
DPM1                                        9.286593e+00                       1.176677e+01                   2.649445e+01                       1.148826e+01                   1.273634e+01
SCYL3                                       7.222905e+00                       4.978251e+00                   0.000000e+00                       2.513056e+00                   4.548694e-01
C1orf112                                    6.878957e-01                       0.000000e+00                   0.000000e+00                       3.590080e-01                   0.000000e+00
FGR                                         5.262402e+01                       3.258491e+01                   1.519015e+02                       5.636426e+01                   5.276484e+01
CFH                                         4.471322e+00                       5.430819e+00                   8.831484e+00                       2.154048e+00                   5.913302e+00
FUCA2                                       1.582160e+01                       2.851180e+01                   1.413037e+01                       1.376197e+01                   2.592755e+01
GCLC                                        1.685345e+01                       2.851180e+01                   2.296186e+01                       3.637948e+01                   9.552256e+00
NFYA                                        3.645847e+01                       1.493475e+01                   0.000000e+00                       2.249783e+01                   2.865677e+01
STPG1                                       7.910801e+00                       1.221934e+01                   0.000000e+00                       5.744128e+00                   2.729216e+00
NIPAL3                                      1.238212e+01                       4.978251e+00                   1.766297e+01                       1.160793e+01                   7.277910e+00
LAS1L                                       2.682793e+01                       3.620546e+01                   1.766297e+01                       4.451699e+01                   4.594180e+01
ENPP4                                       4.815270e+00                       1.629246e+01                   0.000000e+00                       6.940821e+00                   6.368171e+00
SEMA3F                                      3.370689e+01                       1.855530e+01                   2.472816e+01                       1.579635e+01                   1.410095e+01
ANKIB1                                      1.410186e+01                       2.081814e+01                   1.413037e+01                       1.926676e+01                   7.732779e+00
CYP51A1                                     1.169423e+01                       1.810273e+00                   4.415742e+01                       8.137515e+00                   1.637530e+01
KRIT1                                       1.341397e+01                       9.956502e+00                   1.942927e+01                       1.340297e+01                   1.228147e+01
RAD52                                       1.272607e+01                       1.040907e+01                   3.355964e+01                       8.017845e+00                   1.319121e+01
MYH16                                       0.000000e+00                       0.000000e+00                   0.000000e+00                       0.000000e+00                   0.000000e+00
BAD                                         5.950298e+01                       5.068764e+01                   3.709223e+01                       5.181682e+01                   2.820190e+01
LAP3                                        2.338846e+01                       4.344655e+01                   4.769002e+01                       4.355964e+01                   6.550119e+01
CD99                                        2.414514e+02                       2.086340e+02                   1.713308e+02                       2.198326e+02                   1.983230e+02
HS3ST1                                      8.598697e+00                       7.241092e+00                   2.826075e+01                       6.940821e+00                   1.501069e+01
AOC1                                        8.942645e+00                       0.000000e+00                   0.000000e+00                       7.180160e-01                   0.000000e+00
WNT16                                       0.000000e+00                       0.000000e+00                   0.000000e+00                       7.180160e-01                   4.548694e-01
HECW1                                       1.238212e+01                       4.073114e+00                   1.766297e+00                       1.914709e+00                   5.003563e+00
MAD1L1                                      5.159218e+00                       5.430819e+00                   2.119556e+01                       8.616192e+00                   9.097387e+00
LASP1                                       3.755911e+02                       2.656576e+02                   3.426616e+02                       3.999349e+02                   3.270511e+02
SNX11                                       4.815270e+00                       4.978251e+00                   2.119556e+01                       1.041123e+01                   1.683017e+01
TMEM176A                                    2.614004e+01                       3.756316e+01                   4.239112e+01                       2.632725e+01                   8.369596e+01
                          X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte X160_Tibia_non.sclerotic_adipocyte
TSPAN6                                          9.450250e+00                   2.491723e+00                       9.861323e+00                   8.888556e+00                       1.136393e+01
TNMD                                            1.512040e+00                   0.000000e+00                       1.195312e+00                   1.437855e+00                       1.010127e+00
DPM1                                            7.434197e+00                   9.254973e+00                       1.180370e+01                   1.111069e+01                       1.304748e+01
SCYL3                                           4.788127e+00                   1.779802e+00                       5.378903e+00                   3.921422e-01                       2.272787e+00
C1orf112                                        1.260033e+00                   0.000000e+00                       2.988280e-01                   2.614281e-01                       6.734183e-01
FGR                                             3.704498e+01                   2.598512e+01                       1.942382e+01                   2.862638e+01                       1.414178e+01
CFH                                             5.040134e-01                   1.067881e+00                       2.091796e+00                   2.091425e+00                       2.188609e+00
FUCA2                                           1.751446e+01                   7.475170e+00                       1.688378e+01                   1.908425e+01                       1.641457e+01
GCLC                                            3.187884e+01                   2.634108e+01                       3.346873e+01                   4.261278e+01                       3.737472e+01
NFYA                                            4.611722e+01                   2.527319e+01                       2.794041e+01                   3.150209e+01                       3.274496e+01
STPG1                                           9.450250e+00                   1.423842e+00                       3.735350e+00                   5.882132e+00                       8.249374e+00
NIPAL3                                          2.381463e+01                   8.543052e+00                       8.666011e+00                   1.084927e+01                       9.764565e+00
LAS1L                                           3.742299e+01                   5.019043e+01                       3.959470e+01                   4.143635e+01                       3.686965e+01
ENPP4                                           7.560200e+00                   3.559605e+00                       6.723629e+00                   4.052136e+00                       6.060765e+00
SEMA3F                                          3.313888e+01                   3.203644e+01                       2.689452e+01                   1.869211e+01                       2.104432e+01
ANKIB1                                          2.457065e+01                   1.530630e+01                       2.569920e+01                   1.751568e+01                       2.584243e+01
CYP51A1                                         8.568227e+00                   1.495034e+01                       1.120605e+01                   2.705781e+01                       1.481520e+01
KRIT1                                           8.694230e+00                   2.242551e+01                       1.882616e+01                   1.516283e+01                       8.586083e+00
RAD52                                           7.056187e+00                   1.495034e+01                       1.210253e+01                   6.274275e+00                       1.094305e+01
MYH16                                           0.000000e+00                   0.000000e+00                       0.000000e+00                   1.307141e+00                       0.000000e+00
BAD                                             4.107709e+01                   6.514077e+01                       6.439743e+01                   4.980205e+01                       5.833486e+01
LAP3                                            5.682751e+01                   4.129142e+01                       3.989353e+01                   4.457349e+01                       3.358674e+01
CD99                                            2.489826e+02                   3.118214e+02                       2.435448e+02                   2.509710e+02                       2.438616e+02
HS3ST1                                          1.083629e+01                   1.673014e+01                       1.479198e+01                   9.542126e+00                       1.010127e+01
AOC1                                            1.260033e+00                   1.067881e+00                       5.976559e-01                   5.228562e-01                       0.000000e+00
WNT16                                           6.300167e-01                   0.000000e+00                       0.000000e+00                   0.000000e+00                       0.000000e+00
HECW1                                           6.300167e+00                   3.203644e+00                       7.470699e+00                   1.437855e+01                       8.754438e+00
MAD1L1                                          7.434197e+00                   7.831131e+00                       6.873043e+00                   3.921422e+00                       7.491779e+00
LASP1                                           3.763720e+02                   2.762253e+02                       3.133211e+02                   3.635158e+02                       4.629751e+02
SNX11                                           9.828260e+00                   1.210266e+01                       1.299902e+01                   8.888556e+00                       8.754438e+00
TMEM176A                                        2.772073e+01                   2.883280e+01                       1.733202e+01                   2.222139e+01                       1.734052e+01
                          X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6                                      8.849039e+00                       7.814302e+00                   6.966786e+00                           9.673851                   1.992373e+00
TNMD                                        3.356532e+00                       9.494012e-01                   0.000000e+00                           0.000000                   0.000000e+00
DPM1                                        1.271414e+01                       1.942621e+01                   8.866819e+00                          13.088151                   3.320622e+00
SCYL3                                       3.356532e+00                       3.213358e+00                   2.406708e+00                          10.811951                   3.984746e+00
C1orf112                                    8.137048e-01                       6.572778e-01                   1.140020e+00                           0.000000                   0.000000e+00
FGR                                         2.115632e+01                       4.265002e+01                   4.541078e+01                          25.607251                   1.338211e+02
CFH                                         3.865098e+00                       2.190926e+00                   1.646695e+00                           1.138100                   1.328249e+00
FUCA2                                       1.566382e+01                       1.124675e+01                   1.152686e+01                          15.933401                   3.353828e+01
GCLC                                        3.407389e+01                       2.621808e+01                   2.780381e+01                          22.192951                   2.058785e+01
NFYA                                        3.509102e+01                       4.089728e+01                   2.989385e+01                          13.088151                   1.494280e+01
STPG1                                       8.340474e+00                       4.747006e+00                   4.433410e+00                           7.397650                   6.641243e+00
NIPAL3                                      1.047645e+01                       1.205009e+01                   1.342690e+01                           5.690500                   1.527486e+01
LAS1L                                       4.261779e+01                       3.914454e+01                   2.704380e+01                          26.745352                   4.383221e+01
ENPP4                                       3.051393e+00                       5.258222e+00                   4.306741e+00                           3.414300                   2.656497e+00
SEMA3F                                      2.756425e+01                       3.395935e+01                   3.407392e+01                          11.381001                   2.689704e+01
ANKIB1                                      1.627410e+01                       1.833075e+01                   1.634028e+01                           5.121450                   1.627105e+01
CYP51A1                                     1.739294e+01                       1.453314e+01                   1.399691e+01                           3.414300                   1.029393e+01
KRIT1                                       1.800322e+01                       1.095463e+01                   1.209687e+01                          15.364351                   1.095805e+01
RAD52                                       1.108673e+01                       1.168494e+01                   1.064018e+01                           2.276200                   1.062599e+01
MYH16                                       0.000000e+00                       3.651543e-01                   8.866819e-01                           2.276200                   0.000000e+00
BAD                                         4.627946e+01                       4.520610e+01                   4.211739e+01                          57.474053                   4.183983e+01
LAP3                                        3.824412e+01                       4.367246e+01                   4.281407e+01                          17.640551                   3.586271e+01
CD99                                        2.718791e+02                       1.852063e+02                   1.983634e+02                         207.703262                   2.782681e+02
HS3ST1                                      8.747326e+00                       1.161191e+01                   1.165353e+01                           6.828600                   1.527486e+01
AOC1                                        0.000000e+00                       4.381852e-01                   1.140020e+00                           0.000000                   3.320622e-01
WNT16                                       7.119917e-01                       2.190926e-01                   0.000000e+00                           0.000000                   7.305368e+00
HECW1                                       1.108673e+01                       7.449148e+00                   4.116737e+00                           1.707150                   0.000000e+00
MAD1L1                                      8.849039e+00                       5.185191e+00                   8.676816e+00                           2.845250                   8.301554e+00
LASP1                                       3.641329e+02                       3.119878e+02                   3.380791e+02                         476.294877                   3.181156e+02
SNX11                                       5.289081e+00                       6.134592e+00                   6.650114e+00                           6.259550                   2.490466e+01
TMEM176A                                    5.319595e+01                       2.614505e+01                   5.953436e+01                          11.950051                   2.424054e+01
                          X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte
TSPAN6                                          2.352198e+01                      1.358506e+00
TNMD                                            0.000000e+00                      0.000000e+00
DPM1                                            1.447507e+01                      8.490665e+00
SCYL3                                           4.975804e+00                      0.000000e+00
C1orf112                                        4.523458e-01                      0.000000e+00
FGR                                             2.397433e+01                      1.005295e+02
CFH                                             4.523458e+00                      2.377386e+00
FUCA2                                           1.311803e+01                      1.154730e+01
GCLC                                            1.492741e+01                      3.158527e+01
NFYA                                            2.080791e+01                      3.498154e+01
STPG1                                           9.499262e+00                      6.792532e-01
NIPAL3                                          1.673679e+01                      1.596245e+01
LAS1L                                           3.166421e+01                      4.618922e+01
ENPP4                                           2.261729e+00                      7.811412e+00
SEMA3F                                          2.714075e+00                      2.071722e+01
ANKIB1                                          2.804544e+01                      1.698133e+01
CYP51A1                                         4.975804e+00                      1.596245e+01
KRIT1                                           1.899852e+01                      7.471785e+00
RAD52                                           9.046916e-01                      3.735893e+00
MYH16                                           0.000000e+00                      0.000000e+00
BAD                                             8.096990e+01                      4.245333e+01
LAP3                                            3.935409e+01                      3.260415e+01
CD99                                            2.505996e+02                      2.224554e+02
HS3ST1                                          8.594570e+00                      2.717013e+01
AOC1                                            0.000000e+00                      0.000000e+00
WNT16                                           1.809383e+00                      2.717013e+00
HECW1                                           9.499262e+00                      5.434026e+00
MAD1L1                                          6.332841e+00                      1.052842e+01
LASP1                                           3.772564e+02                      2.784938e+02
SNX11                                           5.428150e+00                      8.830292e+00
TMEM176A                                        1.990322e+01                      2.343424e+01
 [ reached getOption("max.print") -- omitted 23227 rows ]

$tibia_adipocytes_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept)   batchX104   batchX105  batchX109   batchX128  batchX130  batchX144   batchX148  batchX149   batchX151  batchX155  batchX156  batchX159  batchX160   batchX161   batchX163  batchX164    batchX99
TSPAN6     -11.66177 -0.62295592  0.36522127  0.3489849 -0.21180216 -0.2860687 -0.1346908  0.02424395  0.5101485 -1.80082953 -0.1420072 -0.2424379  0.2648817  0.3274959  0.02708262 -0.32928163  1.0052453 -1.82929541
TNMD       -15.81852 -1.69556791  4.04261334  1.5869947 -1.36440513 -1.4717734 -0.2452323  1.27982699  2.5776436 -1.49814352 -1.4504825  2.0734943  3.4991815  4.2641287  1.50009573 -0.93534616 -1.6955679 -1.69556791
DPM1       -11.43940  0.16286130 -0.35888522  0.3880371  0.03714267  0.1324860  0.2014723  0.64959355  0.1324769  0.57782325  0.1633210 -0.2093787  0.1104829  0.2279832  0.30478983 -0.27635455  0.2980255 -0.23423198
SCYL3      -11.12108 -0.39334493 -0.67199147 -1.4048301 -1.22853414 -2.2241578 -1.1030944 -1.40657102 -0.7234495 -1.45998083 -2.0655106 -1.3049623 -1.5628729 -1.3192803 -1.39720638 -0.52120525 -1.0848820 -6.39301023
C1orf112   -17.45450 -0.05958904 -0.02555592  4.6687069 -0.04015864  2.7046401  4.0344145  4.27487472  2.6122500 -0.04712352  2.2608111  3.3021214  2.4793114  3.4073225  3.59787960 -0.02292444  2.8989691 -0.05958904
            groupTSA
TSPAN6   -0.34526954
TNMD     -1.69556791
DPM1     -0.09225483
SCYL3    -0.51948440
C1orf112 -0.05958904
23253 more rows ...

$fitted.values
         X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6                     1.800000e+01                       1.200000e+01                       1.757325e+01                   1.733060e+01                          52.778484                      37.820425
TNMD                       1.158125e-08                       1.020338e-08                       1.350688e+01                   2.275058e+00                           2.806181                       0.343448
DPM1                       2.900000e+01                       3.300000e+01                       1.062668e+01                   1.351289e+01                          68.554845                      63.342685
SCYL3                      2.600000e+01                       2.600000e+01                       1.069219e+01                   8.820703e+00                          15.628570                       9.368367
C1orf112                   2.594062e-08                       2.284082e-08                       1.323546e-08                   1.728447e-08                          12.077075                      11.460054
         X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6                         1.550983e+01                   5.224733e+00                       2.290853e+01                   4.549621e+00                        103.7951316                    44.60706843
TNMD                           1.537838e-08                   8.847967e-10                       2.264966e-08                   7.682731e-10                          0.8652398                     0.06350955
DPM1                           2.488324e+01                   1.080819e+01                       4.356602e+01                   1.115616e+01                        181.6611231                   100.66477252
SCYL3                          9.629576e+00                   2.713559e+00                       5.597135e+00                   9.298630e-01                         67.6598688                    24.32388791
C1orf112                       2.002831e-08                   8.934220e-09                       1.316152e+00                   3.461303e-01                         20.2504100                    11.52433684
         X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6                            53.142827                     4.24947175                          66.513180                     29.4632668                       3.089862e+00                   5.597409e-01
TNMD                               2.807634                     0.03834481                           8.473526                      0.6410814                       1.317628e-08                   4.076775e-10
DPM1                             124.254754                    12.81126831                          56.906651                     32.5031188                       4.233013e+01                   9.887496e+00
SCYL3                             21.737053                     1.45400569                          33.303165                     12.3405306                       7.542126e+00                   1.142923e+00
C1orf112                          11.273342                     1.19370876                           1.543938                      0.9056463                       1.949677e-08                   4.676985e-09
         X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6                         6.227506e+01                   1.158345e+01                          53.459220                     13.3792082                          75.022863                      60.630357
TNMD                           5.753792e-08                   1.827906e-09                           8.638478                      0.3692503                          42.219560                       5.827551
DPM1                           1.056929e+02                   2.534886e+01                          69.084438                     22.2934276                          80.286750                      83.662183
SCYL3                          1.545144e+01                   2.404185e+00                          31.658488                      6.6278567                          20.549605                      13.892331
C1orf112                       1.918051e+00                   4.724319e-01                           5.481824                      1.8167214                           1.933889                       2.069586
         X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6                           141.785495                      82.961651                         120.918370                      98.579460                       1.084580e+01                   1.314075e+01
TNMD                             168.374808                      16.826685                           7.755859                       1.079941                       1.660587e-08                   3.436340e-09
DPM1                             160.315251                     120.950939                         199.554207                     209.770233                       1.430145e+01                   2.234228e+01
SCYL3                             46.784009                      22.899087                          49.807517                      33.967547                       1.541718e+01                   1.562567e+01
C1orf112                           9.151423                       7.090709                          12.843483                      13.865400                       1.648242e-08                   2.644448e-08
         X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte
TSPAN6                         5.200000e+01                      4.000000e+00
TNMD                           8.641161e-09                      1.150906e-08
DPM1                           3.200000e+01                      2.500000e+01
SCYL3                          1.100000e+01                      1.681699e-07
C1orf112                       1.000000e+00                      2.576369e-08
23253 more rows ...

$deviance
[1]  9.772060  8.017749  9.392321 13.662324  9.226843
23253 more elements ...

$iter
[1]  7 19  6 18 18
23253 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
23253 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6                               18                                 12                                 26                              9                                 43                             45
TNMD                                  0                                  0                                 10                              3                                  4                              0
DPM1                                 29                                 33                                  6                             19                                 70                             62
SCYL3                                26                                 26                                 14                              6                                 10                             13
C1orf112                              0                                  0                                  0                              0                                  1                             22
         X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6                                   16                              5                                 28                              3                                 65                             62
TNMD                                      0                              0                                  0                              0                                  1                              0
DPM1                                     34                              6                                 38                             13                                174                            105
SCYL3                                     4                              5                                  8                              0                                 50                             31
C1orf112                                  0                              0                                  2                              0                                 16                             14
         X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6                                   33                              7                                 59                             33                                  4                              0
TNMD                                      3                              0                                 13                              0                                  0                              0
DPM1                                    101                             16                                 66                             27                                 26                             15
SCYL3                                    18                              2                                 12                             21                                 11                              0
C1orf112                                 19                              0                                  0                              2                                  0                              0
         X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6                                   43                             16                                 75                              7                                 66                             68
TNMD                                      0                              0                                 12                              0                                  8                             11
DPM1                                     96                             28                                 59                             26                                 79                             85
SCYL3                                    21                              1                                 38                              5                                 36                              3
C1orf112                                  3                              0                                 10                              0                                  2                              2
         X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6                                  135                             87                                107                            110                                 17                              6
TNMD                                     12                             33                                 13                              0                                  0                              0
DPM1                                    155                            125                                266                            140                                 23                             10
SCYL3                                    27                             33                                 44                             38                                 19                             12
C1orf112                                  8                              8                                  9                             18                                  0                              0
         X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte
TSPAN6                                   52                                 4
TNMD                                      0                                 0
DPM1                                     32                                25
SCYL3                                    11                                 0
C1orf112                                  1                                 0
23253 more rows ...

$unshrunk.coefficients
         (Intercept)   batchX104    batchX105  batchX109   batchX128 batchX130  batchX144   batchX148  batchX149   batchX151  batchX155 batchX156  batchX159  batchX160   batchX161    batchX163  batchX164     batchX99
TSPAN6     -11.66440 -0.62569730  0.365874987  0.3500012 -0.21274568 -0.287283 -0.1350862  0.02409791  0.5114728 -1.81580236 -0.1425740 -0.243640  0.2656463  0.3283730  0.02713032 -0.331121234  1.0068232  -1.84472633
TNMD       -31.06136 -2.11419066 19.499657010 16.8126824 -1.54756253 -1.624953 14.4747065 16.48041730 17.8479798 -1.69181576 -1.5479963 17.330628 19.0876974 19.8972105 16.67742364 -1.231448112 -2.1141891  -2.11419165
DPM1       -11.44165  0.16315920 -0.359879003  0.3887872  0.03723045  0.132741  0.2018933  0.65070428  0.1327405  0.57882577  0.1636583 -0.209974  0.1107135  0.2284554  0.30535613 -0.277282786  0.2985709  -0.23488928
SCYL3      -11.11817 -0.39873977 -0.677221939 -1.4132341 -1.23561293 -2.242770 -1.1092444 -1.41609926 -0.7265072 -1.46965720 -2.0826652 -1.313785 -1.5755373 -1.3266333 -1.40605181 -0.525649128 -1.0927576 -19.37554397
C1orf112   -32.30304 -0.06668053 -0.002228838 19.5138467 -0.04169894 17.494560 18.8693098 19.11219566 17.3870494 -0.05830585 17.0158144 18.117519 17.2460263 18.2266072 18.42349128  0.002769465 17.6942196  -0.06668022
            groupTSA
TSPAN6   -0.34670591
TNMD     -2.11399556
DPM1     -0.09252625
SCYL3    -0.52521349
C1orf112 -0.06589317
23253 more rows ...

$df.residual
[1] 13 13 13 13 13
23253 more elements ...

$design
                                   (Intercept) batchX104 batchX105 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99
X102_tibia_sclerotic_adipocyte               1         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0
X104_tibia_non.sclerotic_adipocyte           1         1         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0
X105_tibia_non.sclerotic_adipocyte           1         0         1         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0
X105_tibia_sclerotic_adipocyte               1         0         1         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0
X109_tibia_non.sclerotic_adipocyte           1         0         0         1         0         0         0         0         0         0         0         0         0         0         0         0         0        0
                                   groupTSA
X102_tibia_sclerotic_adipocyte            1
X104_tibia_non.sclerotic_adipocyte        0
X105_tibia_non.sclerotic_adipocyte        0
X105_tibia_sclerotic_adipocyte            1
X109_tibia_non.sclerotic_adipocyte        0
27 more rows ...

$offset
         [,1]   [,2]    [,3]    [,4]    [,5]     [,6]     [,7]     [,8]     [,9]    [,10]   [,11]    [,12]    [,13]   [,14]    [,15]    [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]    [,25]
[1,] 14.90148 14.775 14.1649 14.4977 15.2805 15.29395 14.61862 13.87725 15.08319 13.81343 16.4419 15.94408 15.61328 13.4338 15.35033 14.88278 14.60833 13.24663 15.93853 14.60326 15.88696 14.84845 15.71654 15.85025 16.29034
        [,26]    [,27]    [,28]   [,29]    [,30]    [,31]    [,32]
[1,] 16.10111 16.43238 16.57484 14.3793 14.91794 14.60882 14.89542
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 32
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23253 more rows ...

$dispersion
[1] 0.2872179 1.5359262 0.2041911 0.4959211 1.5430748
23253 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1] 3.022363 0.176057 3.656305 2.044776 0.169501
23253 more elements ...

$df.residual.zeros
[1] 13  8 13 13  9
23253 more elements ...

$df.prior
[1] 159.471 159.471 159.471 159.471 159.471
23253 more elements ...

$var.post
[1] 1.244144 1.361507 1.149438 1.355407 1.360682
23253 more elements ...

$var.prior
[1] 1.284288 1.379531 1.184243 1.380226 1.379615
23253 more elements ...

$samples
27 more rows ...

$genes
23253 more rows ...


$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.8391389

$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.8601605

$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 1.394509

$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.443521


$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 1.699138 1.699138

$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 1.1568013 0.8700811



$tibia_adipocytes_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$tibia_adipocytes_sclerotic_vs_non_sclerotic$boxplot_gg


$tibia_pellet_sclerotic_vs_non_sclerotic
$tibia_pellet_sclerotic_vs_non_sclerotic$name
[1] "TSP-vs-TNSP"

$tibia_pellet_sclerotic_vs_non_sclerotic$results
Coefficient:  groupTSP 

$tibia_pellet_sclerotic_vs_non_sclerotic$colsums_samples

$tibia_pellet_sclerotic_vs_non_sclerotic$normalized_matrix
                          X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet
TSPAN6                                       2.369877e-01                8.947041e+00                    5.291329e+00                6.836571e+00                    7.008758e+00                    3.420468
DPM1                                         1.398228e+01                1.342056e+01                    1.774152e+01                6.836571e+00                    1.429787e+01                   13.111794
SCYL3                                        4.818750e+00                3.195372e+00                    2.178783e+00                6.215065e+00                    2.242803e+00                    3.420468
C1orf112                                     5.608709e+00                0.000000e+00                    2.801292e+00                0.000000e+00                    5.607006e-01                    0.000000
FGR                                          1.055543e+03                1.990717e+02                    1.179655e+02                6.960872e+01                    1.553141e+02                   81.521152
CFH                                          7.109631e-01                3.514909e+00                    1.556273e+00                2.486026e+00                    6.541507e-01                    3.990546
FUCA2                                        1.090143e+01                1.853316e+01                    5.913839e+00                1.719501e+01                    1.055986e+01                   19.952730
GCLC                                         4.565963e+01                1.917223e+01                    1.649650e+01                1.035844e+01                    2.691363e+01                    5.130702
NFYA                                         5.379621e+01                3.419048e+01                    3.859558e+01                3.148966e+01                    3.261409e+01                   38.195225
STPG1                                        2.053894e+00                6.071206e+00                    3.423801e+00                8.286753e-01                    4.859406e+00                   15.392106
NIPAL3                                       1.658914e+01                1.022519e+01                    4.980075e+00                1.222296e+01                    1.654067e+01                   27.933821
LAS1L                                        4.700256e+01                3.674677e+01                    7.189983e+01                2.216706e+01                    4.831370e+01                   22.803119
ENPP4                                        1.224437e+01                4.473520e+00                    3.112547e+00                3.314701e+00                    7.943259e+00                    3.420468
SEMA3F                                       1.342930e+00                2.204806e+01                    7.501237e+01                5.179220e+01                    5.719147e+01                   31.354289
ANKIB1                                       7.188627e+00                1.342056e+01                    1.245019e+01                1.056561e+01                    1.654067e+01                    9.691326
CYP51A1                                      6.082685e+00                7.988429e+00                    1.276144e+01                8.701090e+00                    6.915308e+00                   10.261404
KRIT1                                        1.019047e+01                9.266578e+00                    1.649650e+01                1.636634e+01                    1.644722e+01                    9.121248
RAD52                                        1.153340e+01                1.917223e+00                    7.470112e+00                1.367314e+01                    1.055986e+01                    3.990546
MYH16                                        0.000000e+00                0.000000e+00                    0.000000e+00                0.000000e+00                    1.869002e-01                    0.000000
BAD                                          2.172387e+01                5.336271e+01                    2.241034e+01                3.874057e+01                    2.794158e+01                   36.484991
LAP3                                         1.516721e+01                1.469871e+01                    3.361550e+01                2.361725e+01                    3.709969e+01                   46.746395
CD99                                         7.315021e+01                1.907637e+02                    1.494022e+02                3.530157e+02                    2.032540e+02                  280.478370
HS3ST1                                       1.421926e+00                1.853316e+01                    1.462897e+01                3.874057e+01                    2.859573e+01                   36.484991
AOC1                                         4.344775e+00                4.473520e+00                    6.225093e-01                4.143376e-01                    1.682102e+00                    0.570078
WNT16                                        7.899590e-02                1.310102e+01                    0.000000e+00                4.143376e-01                    1.401752e+00                   29.073977
HECW1                                        6.319672e-01                2.556297e+00                    4.980075e+00                4.143376e+00                    1.495202e+00                    4.560624
MAD1L1                                       2.022295e+01                1.885269e+01                    5.913839e+00                9.322597e+00                    1.233541e+01                    5.700780
LASP1                                        2.978146e+02                2.083382e+02                    1.715013e+02                3.030880e+02                    2.433441e+02                  145.939965
SNX11                                        6.240676e+00                3.514909e+00                    4.046311e+00                7.043740e+00                    8.690860e+00                    7.411014
TMEM176A                                     3.080840e+00                6.710281e+00                    1.338395e+01                4.329828e+01                    1.850312e+01                   15.962184
M6PR                                         4.044590e+01                2.204806e+01                    2.645665e+01                2.403158e+01                    2.420358e+01                   24.513353
KLHL13                                       7.899590e-01                8.627504e+00                    9.337640e-01                4.143376e-01                    1.027951e+00                    1.140156
CYP26B1                                      2.527869e+00                4.313752e+01                    1.092504e+02                4.557714e+01                    1.831622e+01                   45.036161
                          X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet
TSPAN6                                       4.773253e-01                1.249578e+01                    2.506446e+00                6.273754e+00                    7.801261e-01                    7.871938e+00
DPM1                                         1.897368e+01                2.637997e+01                    2.101558e+01                1.283268e+01                    1.633676e+01                    1.049592e+01
SCYL3                                        1.909301e+00                9.718936e+00                    3.663267e+00                5.418242e+00                    1.697921e+00                    2.099183e+00
C1orf112                                     2.744620e+00                0.000000e+00                    3.566865e+00                1.140683e+00                    3.441733e+00                    0.000000e+00
FGR                                          3.970153e+02                7.913991e+01                    3.379846e+02                4.762350e+01                    6.134544e+02                    1.280502e+02
CFH                                          7.159879e-01                5.553678e+00                    3.856071e-01                4.562730e+00                    2.753386e-01                    7.347142e+00
FUCA2                                        1.169447e+01                2.776839e+00                    1.773792e+01                4.847901e+00                    9.177954e+00                    6.297550e+00
GCLC                                         6.026232e+01                2.637997e+01                    4.685126e+01                7.129266e+00                    9.659796e+01                    1.469428e+01
NFYA                                         3.639605e+01                2.499155e+01                    3.672907e+01                2.623570e+01                    4.928561e+01                    5.772754e+00
STPG1                                        3.699271e+00                1.249578e+01                    4.338079e+00                1.711024e+00                    4.497197e+00                    2.099183e+00
NIPAL3                                       1.718371e+01                1.666103e+01                    1.754512e+01                2.081746e+01                    1.808057e+01                    8.396734e+00
LAS1L                                        3.818602e+01                3.609891e+01                    4.579084e+01                3.992389e+01                    5.571018e+01                    3.096295e+01
ENPP4                                        5.727903e+00                4.165258e+00                    7.615739e+00                3.422048e+00                    2.891055e+00                    2.099183e+00
SEMA3F                                       2.852019e+01                1.804945e+01                    9.061766e+00                3.479082e+01                    9.545072e+00                    3.096295e+01
ANKIB1                                       9.904500e+00                1.110736e+01                    6.940927e+00                2.338399e+01                    7.893040e+00                    6.297550e+00
CYP51A1                                      7.398542e+00                0.000000e+00                    4.916490e+00                9.410631e+00                    7.525922e+00                    7.871938e+00
KRIT1                                        9.665837e+00                2.776839e+00                    1.301424e+01                1.112165e+01                    1.693332e+01                    1.416949e+01
RAD52                                        1.073982e+01                1.249578e+01                    1.262863e+01                5.133072e+00                    1.330803e+01                    9.971121e+00
MYH16                                        0.000000e+00                0.000000e+00                    0.000000e+00                2.566536e+00                    9.177954e-02                    0.000000e+00
BAD                                          3.031016e+01                2.221471e+01                    2.275082e+01                4.819384e+01                    2.097162e+01                    5.510356e+01
LAP3                                         3.198079e+01                1.943787e+01                    2.660689e+01                2.024712e+01                    2.069629e+01                    1.994224e+01
CD99                                         1.021476e+02                1.249578e+02                    1.252259e+02                2.395433e+02                    8.420773e+01                    2.802410e+02
HS3ST1                                       7.995198e+00                1.527261e+01                    4.530883e+00                9.125460e+00                    5.047875e+00                    7.347142e+00
AOC1                                         1.909301e+00                0.000000e+00                    8.676159e-01                0.000000e+00                    5.506772e-01                    1.574388e+00
WNT16                                        1.551307e+00                1.666103e+01                    2.892053e-01                1.425853e+00                    0.000000e+00                    5.772754e+00
HECW1                                        5.966566e-01                1.388419e+00                    1.253223e+00                2.566536e+00                    9.177954e-02                    1.364469e+01
MAD1L1                                       1.563240e+01                1.388419e+01                    1.725592e+01                1.083648e+01                    1.725455e+01                    5.772754e+00
LASP1                                        2.081138e+02                1.332883e+02                    2.322318e+02                2.871668e+02                    2.666654e+02                    1.810546e+02
SNX11                                        6.085897e+00                2.776839e+00                    1.388185e+01                9.695802e+00                    8.168379e+00                    6.297550e+00
TMEM176A                                     6.085897e+00                8.330517e+00                    2.265441e+01                3.963872e+01                    4.405418e+00                    3.253734e+01
M6PR                                         3.699271e+01                1.110736e+01                    3.846430e+01                2.281365e+01                    3.386665e+01                    7.871938e+00
KLHL13                                       7.159879e-01                6.942097e+00                    1.253223e+00                1.140683e+00                    8.260158e-01                    0.000000e+00
CYP26B1                                      1.157514e+01                4.859468e+01                    1.513508e+01                8.897324e+01                    7.067024e+00                    7.294662e+01
                          X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet
TSPAN6                                       9.424599                    1.207567e+01                4.740855e+01                    8.079465e+00                3.757062e+00                    3.001096e+01
DPM1                                         0.000000                    1.380077e+01                4.740855e+00                    1.253710e+01                1.202260e+01                    1.385121e+01
SCYL3                                        1.346371                    6.612869e+00                6.321140e+00                    0.000000e+00                7.514123e-01                    4.617070e+00
C1orf112                                     0.000000                    1.150064e+00                0.000000e+00                    8.358067e-01                0.000000e+00                    1.154268e+00
FGR                                         86.167758                    5.232792e+01                3.160570e+01                    1.317789e+02                8.641242e+01                    5.655911e+01
CFH                                         26.927424                    2.875160e+00                1.580285e+01                    1.114409e+00                1.051977e+01                    8.079873e+00
FUCA2                                       10.770970                    1.523835e+01                0.000000e+00                    6.965056e+00                5.259886e+00                    2.885669e+01
GCLC                                        30.966538                    1.380077e+01                1.264228e+01                    1.504452e+01                1.427683e+01                    2.077682e+01
NFYA                                        30.966538                    4.226486e+01                3.318599e+01                    1.699474e+01                1.127118e+01                    4.386217e+01
STPG1                                        5.385485                    1.092561e+01                6.321140e+00                    8.358067e+00                2.254237e+00                    0.000000e+00
NIPAL3                                      29.620167                    8.050449e+00                2.528456e+01                    2.200958e+01                3.005649e+01                    1.962255e+01
LAS1L                                       41.737508                    2.788906e+01                4.108741e+01                    4.262614e+01                2.479661e+01                    2.193108e+01
ENPP4                                        0.000000                    8.050449e+00                4.740855e+00                    5.572045e-01                1.502825e+00                    0.000000e+00
SEMA3F                                      28.273796                    4.456498e+01                1.738314e+01                    4.206894e+01                3.531638e+01                    5.655911e+01
ANKIB1                                      18.849197                    9.775545e+00                1.422257e+01                    1.532312e+01                9.768360e+00                    4.617070e+00
CYP51A1                                     39.044765                    6.325353e+00                0.000000e+00                    1.142269e+01                1.127118e+01                    6.925605e+00
KRIT1                                       14.810083                    8.625481e+00                0.000000e+00                    1.086549e+01                7.514123e-01                    1.154268e+01
RAD52                                        5.385485                    9.775545e+00                0.000000e+00                    6.129249e+00                2.254237e+00                    0.000000e+00
MYH16                                        0.000000                    0.000000e+00                6.321140e+00                    0.000000e+00                0.000000e+00                    0.000000e+00
BAD                                         78.089531                    4.887773e+01                3.318599e+01                    6.129249e+01                1.577966e+01                    3.347376e+01
LAP3                                         9.424599                    5.089034e+01                2.212399e+01                    2.256678e+01                4.057627e+01                    9.234140e+00
CD99                                       273.313358                    1.581338e+02                2.101779e+02                    1.755194e+02                2.088926e+02                    1.927627e+02
HS3ST1                                      37.698394                    1.638841e+01                3.476627e+01                    1.588033e+01                2.705084e+01                    1.154268e+00
AOC1                                         0.000000                    0.000000e+00                0.000000e+00                    0.000000e+00                1.502825e+00                    1.038841e+01
WNT16                                        0.000000                    0.000000e+00                1.106200e+01                    0.000000e+00                8.265536e+00                    6.925605e+00
HECW1                                        0.000000                    2.300128e+00                7.901426e+00                    4.457636e+00                3.005649e+00                    0.000000e+00
MAD1L1                                       0.000000                    1.236319e+01                0.000000e+00                    1.281570e+01                1.427683e+01                    1.154268e+00
LASP1                                      192.531084                    2.308754e+02                2.670682e+02                    2.178670e+02                2.705084e+02                    1.939169e+02
SNX11                                        2.692742                    9.775545e+00                1.580285e+00                    3.621829e+00                3.005649e+00                    1.154268e+00
TMEM176A                                     9.424599                    2.702651e+01                3.634656e+01                    1.532312e+01                4.358192e+01                    2.193108e+01
M6PR                                        13.463712                    3.248931e+01                1.422257e+01                    2.312399e+01                2.103955e+01                    1.962255e+01
KLHL13                                       0.000000                    2.012612e+00                0.000000e+00                    5.572045e-01                0.000000e+00                    0.000000e+00
CYP26B1                                     44.430250                    3.565199e+01                3.634656e+01                    2.841743e+01                6.236722e+01                    2.654815e+01
                          X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet
TSPAN6                                   1.429542e+01                    5.262119e+00                6.552841e+00                    4.263451e+00                3.224208e+00                    1.959330e+01
DPM1                                     1.965620e+01                    1.195936e+01                9.707912e+00                    1.899174e+01                9.770326e+00                    8.163875e+00
SCYL3                                    8.934639e-01                    2.072956e+00                3.640467e+00                    5.426210e+00                3.908131e+00                    9.796650e+00
C1orf112                                 8.934639e-01                    4.783744e-01                2.426978e-01                    4.263451e+00                5.862196e-01                    0.000000e+00
FGR                                      7.505096e+01                    5.923870e+01                3.470579e+01                    3.410761e+01                4.396647e+01                    8.408791e+01
CFH                                      8.934639e-01                    3.109434e+00                2.912374e+00                    6.976556e+00                5.178273e+00                    8.163875e-01
FUCA2                                    8.934639e+00                    1.642419e+01                2.888104e+01                    1.472829e+01                9.868030e+00                    2.938995e+01
GCLC                                     1.697581e+01                    2.431737e+01                1.893043e+01                    2.558071e+01                2.706380e+01                    2.938995e+01
NFYA                                     1.786928e+01                    2.814436e+01                3.179341e+01                    3.216968e+01                2.559825e+01                    2.204246e+01
STPG1                                    6.254247e+00                    4.066182e+00                9.707912e-01                    5.813797e+00                2.442582e+00                    1.877691e+01
NIPAL3                                   4.467319e+00                    1.259719e+01                8.494423e+00                    4.651038e+00                1.074736e+01                    1.551136e+01
LAS1L                                    5.182090e+01                    3.428350e+01                2.475518e+01                    2.519312e+01                3.488006e+01                    3.837021e+01
ENPP4                                    8.934639e-01                    4.863473e+00                4.125863e+00                    1.240277e+01                1.856362e+00                    0.000000e+00
SEMA3F                                   1.965620e+01                    4.249559e+01                4.975305e+01                    4.573520e+01                7.230041e+01                    4.245215e+01
ANKIB1                                   8.934639e+00                    1.714175e+01                1.067870e+01                    1.511587e+01                1.172439e+01                    1.796053e+01
CYP51A1                                  1.697581e+01                    1.578636e+01                1.917313e+01                    1.937932e+01                1.309224e+01                    1.877691e+01
KRIT1                                    3.573855e+00                    1.028505e+01                1.043601e+01                    1.240277e+01                8.597887e+00                    4.898325e+00
RAD52                                    1.965620e+01                    1.012559e+01                1.310568e+01                    8.914489e+00                8.793294e+00                    1.061304e+01
MYH16                                    0.000000e+00                    7.972907e-02                0.000000e+00                    0.000000e+00                5.862196e-01                    8.163875e-01
BAD                                      6.254247e+01                    3.579835e+01                5.096654e+01                    7.054074e+01                5.275976e+01                    2.122608e+01
LAP3                                     5.450130e+01                    4.839554e+01                3.033723e+01                    3.139450e+01                4.416187e+01                    1.877691e+01
CD99                                     2.876954e+02                    2.217265e+02                4.303032e+02                    1.996070e+02                2.208094e+02                    1.200090e+02
HS3ST1                                   1.608235e+01                    2.216468e+01                2.184280e+01                    4.030899e+01                2.931098e+01                    9.796650e+00
AOC1                                     7.147711e+00                    1.195936e+00                9.707912e-01                    3.488278e+00                0.000000e+00                    0.000000e+00
WNT16                                    2.680392e+00                    4.145912e+00                6.552841e+00                    2.713105e+00                1.172439e+00                    4.081938e+00
HECW1                                    5.360783e+00                    1.355394e+00                7.280934e+00                    9.689662e+00                1.563252e+00                    3.265550e+00
MAD1L1                                   1.429542e+01                    9.886404e+00                4.368561e+00                    1.085242e+01                5.178273e+00                    8.163875e-01
LASP1                                    1.974555e+02                    2.816031e+02                3.152645e+02                    2.166608e+02                2.610631e+02                    2.024641e+02
SNX11                                    1.161503e+01                    7.653991e+00                7.766330e+00                    2.713105e+00                4.689757e+00                    7.347488e+00
TMEM176A                                 6.611633e+01                    2.367953e+01                1.286298e+01                    5.387452e+01                8.568576e+01                    3.592105e+01
M6PR                                     1.161503e+01                    2.096875e+01                2.087201e+01                    2.015450e+01                2.510974e+01                    2.285885e+01
KLHL13                                   2.680392e+00                    9.567488e-01                0.000000e+00                    3.875865e-01                1.172439e+00                    0.000000e+00
CYP26B1                                  2.233660e+01                    3.547944e+01                5.266543e+01                    3.449520e+01                4.719068e+01                    3.673744e+01
                          X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                                   1.582542e+01                    1.497217e+00                    1.320607e+01                5.926308e+00                   9.711409e+00               7.254402e+00
DPM1                                     1.012827e+01                    1.247681e+01                    1.097120e+01                9.482092e+00                   2.631479e+01               3.109029e+01
SCYL3                                    2.532068e+00                    1.996290e+00                    3.250725e+00                4.978098e+00                   1.879628e+00               1.036343e+00
C1orf112                                 1.266034e+00                    0.000000e+00                    1.219022e+00                0.000000e+00                   0.000000e+00               0.000000e+00
FGR                                      5.908158e+01                    6.737479e+01                    4.266576e+01                4.432878e+01                   1.206094e+02               9.534356e+01
CFH                                      2.110056e-01                    9.482377e+00                    4.876087e+00                3.081680e+00                   1.253085e+01               1.036343e+01
FUCA2                                    2.363263e+01                    4.990725e+00                    1.259656e+01                2.489049e+01                   1.879628e+01               0.000000e+00
GCLC                                     1.772447e+01                    7.985160e+00                    1.665996e+01                1.849008e+01                   1.315739e+01               1.450880e+01
NFYA                                     2.489866e+01                    1.547125e+01                    2.763116e+01                1.137851e+01                   1.660338e+01               3.523566e+01
STPG1                                    7.596203e+00                    2.994435e+00                    5.079257e+00                8.296831e+00                   0.000000e+00               9.327088e+00
NIPAL3                                   1.920151e+01                    3.094249e+01                    1.401875e+01                1.540840e+01                   1.472375e+01               1.554515e+01
LAS1L                                    2.764174e+01                    2.794806e+01                    4.002455e+01                3.413553e+01                   3.665274e+01               2.072686e+01
ENPP4                                    5.064135e+00                    5.489797e+00                    1.828533e+00                2.133471e+00                   3.445984e+00               2.072686e+00
SEMA3F                                   4.030208e+01                    2.994435e+01                    4.043089e+01                4.006184e+01                   3.915891e+01               2.383589e+01
ANKIB1                                   1.477039e+01                    1.048052e+01                    1.279973e+01                8.533883e+00                   8.145053e+00               6.218058e+00
CYP51A1                                  1.624743e+01                    1.347496e+01                    1.097120e+01                2.441639e+01                   2.130245e+01               1.865418e+01
KRIT1                                    1.308235e+01                    5.988870e+00                    8.939492e+00                1.232672e+01                   1.566356e+00               2.176320e+01
RAD52                                    1.244933e+01                    8.484232e+00                    3.657065e+00                4.978098e+00                   4.385798e+00               4.145372e+00
MYH16                                    0.000000e+00                    4.491652e+00                    4.063406e-01                0.000000e+00                   0.000000e+00               4.145372e+00
BAD                                      3.903604e+01                    5.988870e+01                    4.185308e+01                5.689255e+01                   5.325612e+01               2.487223e+01
LAP3                                     2.468766e+01                    4.192209e+01                    4.896404e+01                4.290647e+01                   2.067590e+01               4.456275e+01
CD99                                     2.572159e+02                    3.378721e+02                    1.800089e+02                2.652615e+02                   1.873362e+02               1.544151e+02
HS3ST1                                   1.688045e+01                    1.147867e+01                    1.422192e+01                4.006184e+01                   7.831782e+00               1.865418e+01
AOC1                                     0.000000e+00                    4.990725e-01                    1.219022e+00                0.000000e+00                   0.000000e+00               0.000000e+00
WNT16                                    1.202732e+01                    3.144157e+01                    3.271042e+01                5.025509e+01                   1.378394e+01               3.109029e+01
HECW1                                    5.486146e+00                    1.497217e+00                    1.015851e+00                7.348622e+00                   3.759255e+00               6.218058e+00
MAD1L1                                   4.642124e+00                    7.486087e+00                    2.031703e+00                1.019325e+01                   1.566356e+01               1.554515e+01
LASP1                                    2.489866e+02                    2.764862e+02                    2.027639e+02                2.363411e+02                   1.835770e+02               1.792874e+02
SNX11                                    8.018214e+00                    8.484232e+00                    7.517300e+00                4.266942e+00                   6.891968e+00               0.000000e+00
TMEM176A                                 4.093509e+01                    3.493507e+01                    1.848850e+01                2.157176e+01                   1.910955e+01               1.865418e+01
M6PR                                     2.574269e+01                    2.495362e+01                    2.377092e+01                2.868333e+01                   1.722992e+01               3.109029e+01
KLHL13                                   4.009107e+00                    4.990725e-01                    1.422192e+00                3.555785e+00                   0.000000e+00               0.000000e+00
CYP26B1                                  9.347550e+01                    6.837293e+01                    6.074791e+01                9.885081e+01                   5.826846e+01               5.803521e+01
 [ reached getOption("max.print") -- omitted 23994 rows ]

$tibia_pellet_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept)  batchX104  batchX109    batchX128  batchX130   batchX144   batchX148  batchX149  batchX151  batchX155  batchX156  batchX159   batchX160   batchX161  batchX163  batchX164   batchX99   groupTSP
TSPAN6    -12.610185  0.4656040  0.4422852  0.403703919  0.1754379  0.07721806 -1.42111406  0.8163995  1.9487877  0.5237170  1.7986388  0.4312905 -0.01883094  1.54257119 -0.7846454  0.9754909  0.8447905  0.2784391
DPM1      -11.083391  0.1452394 -0.5819926 -0.003630514  0.4987407  0.19237705  0.06287435 -0.8849777 -0.3611997 -0.1129534  0.2262298 -0.2406732  0.01120677 -0.36878805 -0.2061841 -0.2949793  0.7434959 -0.2240774
SCYL3     -12.426941 -0.5980406  0.4075137 -0.378306360  0.2538103  0.10490639 -0.84409581 -0.8038386  0.4695531 -2.6876004 -0.4053860 -0.3610354  0.13565891  0.38868046 -0.6844480  0.0103843 -0.9504596  0.0350321
C1orf112  -12.628526 -0.1477432 -3.1477035 -1.868910431 -0.4231967  0.39337781  0.05645284 -4.5658604 -1.1691027 -1.5266838 -0.2378015 -1.3703593  0.15351523  0.04966391 -4.8451503 -1.3593868 -4.6089035 -1.6974468
FGR        -7.253647 -1.7912528 -1.7319488 -1.544142527 -0.9514118 -1.20217369 -0.14271566 -1.6133817 -2.5670434 -1.5967492 -2.0056865 -2.4538622 -2.52084164 -2.00425301 -2.3512102 -2.4509715 -1.5838103 -0.5866547
24022 more rows ...

$fitted.values
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6                          41.85611                   13.702649                              17                 3.30000e+01                       53.210277                  11.5505717                        33.02783
DPM1                           194.20455                   38.349663                              57                 3.30000e+01                      163.568295                  21.4172458                       211.85433
SCYL3                           50.38540                   12.931923                               7                 3.00000e+01                       29.074051                   4.9479608                        42.99219
C1orf112                        41.13761                    1.651918                               9                 7.83076e-08                        5.037821                   0.1341388                        17.90267
FGR                           8957.13096                 1231.443111                             379                 3.36000e+02                     1616.265906                 147.3399717                      2289.77407
         X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6                     3.7590332                        37.10990                   16.612402                              17                    1.433036e+01                7.396822e+00                       81.278981
DPM1                      14.5442075                       192.95117                   52.101060                             356                    1.203640e+01                3.747495e+00                       37.153314
SCYL3                      3.8361761                        45.85939                   16.094728                              37                    3.369226e+00                1.363424e+00                       22.189098
C1orf112                   0.2499296                        53.21360                    2.921926                              75                    5.729235e-08                3.627342e-09                        3.450147
FGR                      109.4431596                      2205.65288                  414.647998                           13368                    2.685515e+02                5.821239e+01                      188.804816
         X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6                    19.5824623                      20.1331437                   9.8850829                       17.437944                  29.8323314                        64.08281                  27.8775615
DPM1                       5.3993707                      49.1723863                  14.5628556                       16.672386                  17.2046642                       151.17964                  39.6700835
SCYL3                      4.1912293                       0.8735848                   0.3362688                        2.291652                   3.0736429                        34.67399                  11.8257820
C1orf112                   0.1019602                       2.4367929                   0.1467544                        2.329870                   0.4889085                        10.12901                   0.5404858
FGR                       19.1030155                     514.3496706                 106.0539866                       82.468882                  59.2491107                       762.49670                 139.2999750
         X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6                          8.383436                   44.039664                       19.073853                   97.724435                    3.000000e+00                       43.437426                  49.2994999
DPM1                           40.025150                  126.826928                       12.985872                   40.132146                    2.500000e+01                       56.183724                  38.4632066
SCYL3                          11.768332                   48.467387                        7.207121                   28.949380                    4.000000e+00                       19.785543                  17.6051263
C1orf112                       10.169781                    6.552959                        4.602971                    2.892723                    3.250778e-08                        3.924222                   0.5463059
FGR                           146.686261                  323.602013                      116.765917                  251.235289                    1.350000e+02                      300.093927                 143.0327358
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                     2.470622e+01               9.889762e+00
DPM1                       1.031048e+02               2.489515e+01
SCYL3                      4.864856e+00               1.526730e+00
C1orf112                   9.579693e-08               4.703649e-09
FGR                        4.633886e+02               7.789769e+01
24022 more rows ...

$deviance
[1] 24.200853  8.965046  6.471256  8.067473 19.107276
24022 more elements ...

$iter
[1] 11  6  9 18 10
24022 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
24022 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6                                 3                          28                              17                          33                              75                           6                               4
DPM1                                 177                          42                              57                          33                             153                          23                             159
SCYL3                                 61                          10                               7                          30                              24                           6                              16
C1orf112                              71                           0                               9                           0                               6                           0                              23
FGR                                13362                         623                             379                         336                            1662                         143                            3327
         X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6                             9                              26                          22                              17                              15                           7                              42
DPM1                              19                             218                          45                             356                              20                           0                              48
SCYL3                              7                              38                          19                              37                               4                           1                              23
C1orf112                           0                              37                           4                              75                               0                           0                               4
FGR                               57                            3506                         167                           13368                             244                          64                             182
         X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6                            30                              29                           5                              26                          16                              66                          27
DPM1                               3                              45                          16                              12                          22                             150                          40
SCYL3                              4                               0                           1                               4                           1                              26                          15
C1orf112                           0                               3                           0                               1                           1                               6                           1
FGR                               20                             473                         115                              49                          84                             743                         143
         X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6                                11                          33                              24                          75                               3                              65                          25
DPM1                                  49                         100                              10                          48                              25                              54                          40
SCYL3                                 14                          40                              12                          12                               4                              16                          21
C1orf112                              11                           6                               0                           6                               0                               6                           0
FGR                                   88                         450                             103                         280                             135                             210                         187
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                               31                          7
DPM1                                 84                         30
SCYL3                                 6                          1
C1orf112                              0                          0
FGR                                 385                         92
24022 more rows ...

$unshrunk.coefficients
         (Intercept)  batchX104   batchX109    batchX128  batchX130   batchX144   batchX148   batchX149  batchX151  batchX155  batchX156  batchX159   batchX160  batchX161   batchX163    batchX164    batchX99    groupTSP
TSPAN6    -12.619632  0.4701909   0.4455788  0.408045364  0.1756204  0.07877449 -1.44417833   0.8217560  1.9555322  0.5285186  1.8062359  0.4351765 -0.01743710  1.5495737  -0.7922702  0.981732013   0.8504908  0.28082888
DPM1      -11.084958  0.1453547  -0.5835778 -0.003649709  0.4994948  0.19265367  0.06286493  -0.8873633 -0.3619764 -0.1131907  0.2266670 -0.2412049  0.01113898 -0.3695569  -0.2066808 -0.295636426   0.7445070 -0.22468863
SCYL3     -12.434168 -0.6025760   0.4081589 -0.381823806  0.2538249  0.10500699 -0.85193744  -0.8114053  0.4717821 -2.7944625 -0.4086031 -0.3644733  0.13625359  0.3908611  -0.6900518  0.009898445  -0.9599909  0.03747496
C1orf112  -12.636947 -0.1484828 -17.2978979 -1.931917556 -0.4194654  0.45651978  0.05741150 -18.4984082 -1.1866233 -1.5658509 -0.1892849 -1.3922806  0.19304086  0.1452724 -19.1153538 -1.405106264 -18.5002846 -1.81750801
FGR        -7.253665 -1.7914536  -1.7321705 -1.544299809 -0.9514890 -1.20229793 -0.14273999  -1.6135492 -2.5676089 -1.5969128 -2.0059590 -2.4543688 -2.52136627 -2.0045409  -2.3515751 -2.451461283  -1.5839658 -0.58678562
24022 more rows ...

$df.residual
[1] 12 12 12 12 12
24022 more elements ...

$design
                                (Intercept) batchX104 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99 groupTSP
X102_tibia_non.sclerotic_pellet           1         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0        0
X102_tibia_sclerotic_pellet               1         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0        1
X104_tibia_non.sclerotic_pellet           1         1         0         0         0         0         0         0         0         0         0         0         0         0         0         0        0        0
X109_tibia_sclerotic_pellet               1         0         1         0         0         0         0         0         0         0         0         0         0         0         0         0        0        1
X128_tibia_non.sclerotic_pellet           1         0         0         1         0         0         0         0         0         0         0         0         0         0         0         0        0        0
25 more rows ...

$offset
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]    [,12]   [,13]    [,14]    [,15]    [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 16.35387 14.95639 14.98265 15.38973 16.18584 14.37749 15.94136 13.48734 16.15474 15.07018 16.89702 14.46026 13.5181 15.06199 13.35791 15.09348 14.10131 13.67204 13.92816 16.34463 15.23145 14.76333 16.14133 14.01838
        [,25]    [,26]    [,27]    [,28]   [,29]    [,30]
[1,] 15.37138 14.51051 15.40922 15.25499 14.9762 13.77981
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 30
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
24022 more rows ...

$dispersion
[1] 0.3716027 0.2763020 0.7333519 1.5146132 0.1501162
24022 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1] 3.2027643 3.8533938 1.9688435 0.7447871 7.2331615
24022 more elements ...

$df.residual.zeros
[1] 12 12 12 10 12
24022 more elements ...

$df.prior
[1] 50.465175 56.309244 56.309244 56.309244  9.321503
24022 more elements ...

$var.post
[1] 1.366888 1.018743 1.224142 1.276124 1.156304
24022 more elements ...

$var.prior
[1] 1.212362 1.076636 1.370094 1.359481 0.595060
24022 more elements ...

$samples
25 more rows ...

$genes
24022 more rows ...


$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.8260483

$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.9351571

$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 0.8723237

$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 3.548994


$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$text
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 1.179955 1.179955

$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 3.237275 2.925556



$tibia_pellet_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$tibia_pellet_sclerotic_vs_non_sclerotic$boxplot_gg


$tibia_sclerotic_vs_non_sclerotic
$tibia_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"

$tibia_sclerotic_vs_non_sclerotic$results
Coefficient:  groupsclerotic 

$tibia_sclerotic_vs_non_sclerotic$colsums_samples

$tibia_sclerotic_vs_non_sclerotic$normalized_matrix
                          X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6                                       2.665806e-01                   5.996075e+00                9.124057e+00                       4.544512e+00                    5.377963e+00                       1.807617e+01
TNMD                                         0.000000e+00                   0.000000e+00                0.000000e+00                       0.000000e+00                    3.163508e-01                       6.952371e+00
DPM1                                         1.572826e+01                   9.660343e+00                1.368609e+01                       1.249741e+01                    1.803199e+01                       4.171423e+00
SCYL3                                        5.420472e+00                   8.660997e+00                3.258592e+00                       9.846443e+00                    2.214455e+00                       9.733320e+00
C1orf112                                     6.309074e+00                   0.000000e+00                0.000000e+00                       0.000000e+00                    2.847157e+00                       0.000000e+00
FGR                                          1.187350e+03                   3.864137e+01                2.030103e+02                       1.378502e+02                    1.198969e+02                       2.224759e+01
CFH                                          7.997418e-01                   1.332461e+00                3.584451e+00                       4.165803e+00                    1.581754e+00                       1.390474e+00
FUCA2                                        1.226271e+01                   2.598299e+01                1.889983e+01                       1.249741e+01                    6.010665e+00                       4.171423e+00
GCLC                                         5.136120e+01                   2.531676e+01                1.955155e+01                       2.764578e+01                    1.676659e+01                       5.909516e+01
NFYA                                         6.051380e+01                   1.732199e+01                3.486693e+01                       5.339802e+01                    3.922750e+01                       3.337138e+01
STPG1                                        2.310365e+00                   1.065969e+01                6.191325e+00                       3.787093e-01                    3.479859e+00                       6.952371e-01
NIPAL3                                       1.866064e+01                   8.660997e+00                1.042749e+01                       4.165803e+00                    5.061612e+00                       1.599045e+01
LAS1L                                        5.287182e+01                   3.031349e+01                3.747381e+01                       8.748186e+01                    7.307703e+01                       3.406662e+01
ENPP4                                        1.377333e+01                   0.000000e+00                4.562029e+00                       2.272256e+00                    3.163508e+00                       6.952371e-01
SEMA3F                                       1.510623e+00                   3.997383e+01                2.248428e+01                       8.748186e+01                    7.624054e+01                       4.797136e+01
ANKIB1                                       8.086278e+00                   1.332461e+01                1.368609e+01                       1.211870e+01                    1.265403e+01                       1.251427e+01
                          X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6                                      4.489760e+00                       9.815976e+00                   1.012778e+01                6.987206e+00                       7.073169e+00                    7.104785e+00
TNMD                                        1.496587e+00                       9.131141e-01                   0.000000e+00                0.000000e+00                       0.000000e+00                    0.000000e+00
DPM1                                        9.478382e+00                       1.597950e+01                   1.395383e+01                6.987206e+00                       1.503049e+01                    1.449376e+01
SCYL3                                       2.993173e+00                       2.282785e+00                   2.925804e+00                6.352005e+00                       1.768292e+00                    2.273531e+00
C1orf112                                    0.000000e+00                       2.282785e-01                   4.951360e+00                0.000000e+00                       0.000000e+00                    5.683828e-01
FGR                                         6.535095e+01                       3.903563e+01                   8.214757e+01                7.114246e+01                       3.713414e+01                    1.574420e+02
CFH                                         6.485209e+00                       4.109013e+00                   5.176422e+00                2.540802e+00                       1.768292e+00                    6.631133e-01
FUCA2                                       1.297042e+01                       1.164220e+01                   1.755482e+01                1.757388e+01                       1.989329e+01                    1.070454e+01
GCLC                                        8.979520e+00                       3.287211e+01                   3.533471e+01                1.058668e+01                       2.652439e+01                    2.728238e+01
NFYA                                        5.238053e+01                       2.008851e+01                   1.823001e+01                3.218349e+01                       1.635670e+01                    3.306093e+01
STPG1                                       5.487485e+00                       2.739342e+00                   6.301732e+00                8.469340e-01                       1.768292e+00                    4.925985e+00
NIPAL3                                      1.297042e+01                       3.195899e+00                   8.102226e+00                1.249228e+01                       1.237805e+01                    1.676729e+01
LAS1L                                       4.140557e+01                       4.634054e+01                   4.838830e+01                2.265549e+01                       3.492377e+01                    4.897565e+01
ENPP4                                       4.988622e-01                       6.163520e+00                   1.800495e+00                3.387736e+00                       2.210365e+00                    8.052090e+00
SEMA3F                                      3.292491e+01                       1.506638e+01                   2.543199e+01                5.293338e+01                       1.989329e+01                    5.797505e+01
ANKIB1                                      1.446700e+01                       1.369671e+01                   9.902721e+00                1.079841e+01                       1.414634e+01                    1.676729e+01
                          X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6                                      4.639109e+00                3.425506e+00                       7.789427e+00                    5.098613e-01                   2.965000e+00                1.277946e+01
TNMD                                        0.000000e+00                0.000000e+00                       0.000000e+00                    0.000000e+00                   0.000000e+00                0.000000e+00
DPM1                                        5.566931e+00                1.313111e+01                       1.057137e+01                    2.026699e+01                   1.284833e+01                2.697887e+01
SCYL3                                       4.639109e+00                3.425506e+00                       2.225551e+00                    2.039445e+00                   0.000000e+00                9.939583e+00
C1orf112                                    0.000000e+00                0.000000e+00                       5.563876e-01                    2.931702e+00                   0.000000e+00                0.000000e+00
FGR                                         3.247377e+01                8.164123e+01                       2.250588e+02                    4.240771e+02                   1.976667e+02                8.093660e+01
CFH                                         0.000000e+00                3.996424e+00                       1.112775e+00                    7.647919e-01                   3.953334e+00                5.679762e+00
FUCA2                                       1.577297e+01                1.998212e+01                       1.112775e+01                    1.249160e+01                   1.186000e+01                2.839881e+00
GCLC                                        3.618505e+01                5.138259e+00                       3.727797e+01                    6.436999e+01                   2.569667e+01                2.697887e+01
NFYA                                        5.381367e+01                3.825148e+01                       2.726299e+01                    3.887692e+01                   1.680167e+01                2.555893e+01
STPG1                                       2.783466e+00                1.541478e+01                       6.954846e+00                    3.951425e+00                   0.000000e+00                1.277946e+01
NIPAL3                                      8.350397e+00                2.797497e+01                       1.780440e+01                    1.835501e+01                   3.953334e+00                1.703928e+01
LAS1L                                       3.247377e+01                2.283671e+01                       2.921035e+01                    4.078890e+01                   1.087167e+01                3.691845e+01
ENPP4                                       3.711287e+00                3.425506e+00                       1.446608e+01                    6.118336e+00                   3.953334e+00                4.259821e+00
SEMA3F                                      2.041208e+01                3.140047e+01                       4.200727e+01                    3.046421e+01                   1.482500e+01                1.845923e+01
ANKIB1                                      3.154594e+01                9.705600e+00                       1.224053e+01                    1.057962e+01                   1.581334e+01                1.135952e+01
                          X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6                                          4.663119e+00                    2.638924e+00                   7.302665e+00                6.425066e+00                       5.400705e+00                    8.535784e-01
TNMD                                            7.174029e-02                    0.000000e+00                   0.000000e+00                2.044339e+00                       4.909732e-01                    0.000000e+00
DPM1                                            1.248281e+01                    2.212637e+01                   1.236742e+01                1.314218e+01                       1.652943e+01                    1.787494e+01
SCYL3                                           3.587015e+00                    3.856889e+00                   3.651333e+00                5.548920e+00                       2.945839e+00                    1.857788e+00
C1orf112                                        1.147845e+00                    3.755392e+00                   1.648989e+00                1.168194e+00                       3.109497e+00                    3.765787e+00
FGR                                             2.292102e+02                    3.558488e+02                   1.110712e+02                4.877209e+01                       2.459776e+02                    6.712139e+02
CFH                                             1.793507e+00                    4.059884e-01                   2.591268e+00                4.672775e+00                       3.273155e-01                    3.012630e-01
FUCA2                                           1.535242e+01                    1.867546e+01                   1.613653e+01                4.964824e+00                       1.587480e+01                    1.004210e+01
GCLC                                            4.655945e+01                    4.932759e+01                   3.015294e+01                7.301211e+00                       7.282769e+01                    1.056931e+02
NFYA                                            3.099181e+01                    3.867039e+01                   2.697275e+01                2.686846e+01                       4.271467e+01                    5.392607e+01
STPG1                                           7.460991e+00                    4.567369e+00                   1.884559e+00                1.752291e+00                       9.001175e+00                    4.920628e+00
NIPAL3                                          1.528068e+01                    1.847247e+01                   6.595956e+00                2.131954e+01                       1.472920e+01                    1.978293e+01
LAS1L                                           3.594189e+01                    4.821112e+01                   3.474655e+01                4.088678e+01                       3.665933e+01                    6.095554e+01
ENPP4                                           2.726131e+00                    8.018270e+00                   3.415763e+00                3.504581e+00                       4.582417e+00                    3.163261e+00
SEMA3F                                          2.518084e+01                    9.540726e+00                   1.448755e+01                3.562991e+01                       4.778806e+01                    1.044378e+01
ANKIB1                                          1.205237e+01                    7.307790e+00                   1.531204e+01                2.394797e+01                       1.652943e+01                    8.636205e+00
                          X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6                                      1.016659e+01                       1.255970e+01                    7.875201e+00                      11.202808                    9.341971                       1.786584e+00
TNMD                                        0.000000e+00                       2.767391e+00                    0.000000e+00                       0.000000                    0.000000                       0.000000e+00
DPM1                                        2.323792e+01                       1.404983e+01                    1.050027e+01                       9.165934                    0.000000                       1.161279e+01
SCYL3                                       2.904739e+00                       2.554515e+00                    2.100054e+00                       7.129059                    1.334567                       4.913105e+00
C1orf112                                    0.000000e+00                       0.000000e+00                    0.000000e+00                       0.678958                    0.000000                       0.000000e+00
FGR                                         4.560441e+02                       5.194180e+01                    1.281033e+02                      51.940290                   85.412310                       3.215850e+01
CFH                                         0.000000e+00                       5.534782e+00                    7.350188e+00                       4.413227                   26.691347                       5.359751e+00
FUCA2                                       4.357109e+00                       1.681722e+01                    6.300161e+00                      15.616035                   10.676539                       2.813869e+01
GCLC                                        1.219991e+02                       3.406020e+01                    1.470038e+01                      16.634472                   30.695049                       2.813869e+01
NFYA                                        5.809479e+01                       3.086705e+01                    5.775147e+00                      35.984776                   30.695049                       1.473931e+01
STPG1                                       8.714218e+00                       5.109029e+00                    2.100054e+00                       7.808018                    5.338269                       1.205944e+01
NIPAL3                                      5.809479e+00                       8.727925e+00                    8.400214e+00                      12.221245                   29.360482                       4.913105e+00
LAS1L                                       2.178555e+01                       3.427307e+01                    3.097579e+01                      26.479364                   41.371588                       3.573167e+01
ENPP4                                       4.357109e+00                       1.213394e+01                    2.100054e+00                       4.752706                    0.000000                       1.607925e+01
SEMA3F                                      1.742844e+01                       2.703528e+01                    3.097579e+01                      33.268944                   28.025914                       1.831248e+01
ANKIB1                                      0.000000e+00                       1.341120e+01                    6.300161e+00                      13.918640                   18.683943                       2.054571e+01
                          X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6                                       1.194617e+01                   0.000000e+00                4.642600e+01                       5.081543e+00                    8.020405e+00                   7.182311e+00
TNMD                                         0.000000e+00                   0.000000e+00                0.000000e+00                       0.000000e+00                    0.000000e+00                   0.000000e+00
DPM1                                         1.365277e+01                   2.613187e+01                4.642600e+00                       1.134484e+01                    1.244546e+01                   1.256904e+01
SCYL3                                        6.541952e+00                   0.000000e+00                6.190134e+00                       2.481684e+00                    0.000000e+00                   4.488945e-01
C1orf112                                     1.137731e+00                   0.000000e+00                0.000000e+00                       3.545262e-01                    8.296971e-01                   0.000000e+00
FGR                                          5.176675e+01                   1.498227e+02                3.095067e+01                       5.566062e+01                    1.308156e+02                   5.207176e+01
CFH                                          2.844327e+00                   8.710623e+00                1.547533e+01                       2.127157e+00                    1.106263e+00                   5.835628e+00
FUCA2                                        1.507493e+01                   1.393700e+01                0.000000e+00                       1.359017e+01                    6.914143e+00                   2.558698e+01
GCLC                                         1.365277e+01                   2.264762e+01                1.238027e+01                       3.592533e+01                    1.493455e+01                   9.426783e+00
NFYA                                         4.181161e+01                   0.000000e+00                3.249820e+01                       2.221698e+01                    1.687051e+01                   2.828035e+01
STPG1                                        1.080844e+01                   0.000000e+00                6.190134e+00                       5.672420e+00                    8.296971e+00                   2.693367e+00
NIPAL3                                       7.964115e+00                   1.742125e+01                2.476053e+01                       1.146302e+01                    2.184869e+01                   7.182311e+00
LAS1L                                        2.758997e+01                   1.742125e+01                4.023587e+01                       4.396125e+01                    4.231455e+01                   4.533834e+01
ENPP4                                        7.964115e+00                   0.000000e+00                4.642600e+00                       6.854174e+00                    5.531314e-01                   6.284522e+00
SEMA3F                                       4.408707e+01                   2.438974e+01                1.702287e+01                       1.559915e+01                    4.176142e+01                   1.391573e+01
ANKIB1                                       9.670711e+00                   1.393700e+01                1.392780e+01                       1.902624e+01                    1.521111e+01                   7.631206e+00
                          X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6                                   3.695893e+00                       9.342745e+00                    2.915851e+01                   2.459210e+00                1.434330e+01                       9.752715e+00
TNMD                                     0.000000e+00                       1.494839e+00                    0.000000e+00                   0.000000e+00                0.000000e+00                       1.182147e+00
DPM1                                     1.182686e+01                       7.349626e+00                    1.345777e+01                   9.134209e+00                1.972204e+01                       1.167370e+01
SCYL3                                    7.391787e-01                       4.733657e+00                    4.485924e+00                   1.756579e+00                8.964565e-01                       5.319663e+00
C1orf112                                 0.000000e+00                       1.245699e+00                    1.121481e+00                   0.000000e+00                8.964565e-01                       2.955368e-01
FGR                                      8.500555e+01                       3.662356e+01                    5.495257e+01                   2.564605e+01                7.530235e+01                       1.920989e+01
CFH                                      1.034850e+01                       4.982797e-01                    7.850367e+00                   1.053947e+00                8.964565e-01                       2.068758e+00
FUCA2                                    5.174251e+00                       1.731522e+01                    2.803703e+01                   7.377630e+00                8.964565e+00                       1.669783e+01
GCLC                                     1.404439e+01                       3.151619e+01                    2.018666e+01                   2.599736e+01                1.703267e+01                       3.310013e+01
NFYA                                     1.108768e+01                       4.559260e+01                    4.261628e+01                   2.494342e+01                1.792913e+01                       2.763269e+01
STPG1                                    2.217536e+00                       9.342745e+00                    0.000000e+00                   1.405263e+00                6.275196e+00                       3.694210e+00
NIPAL3                                   2.956715e+01                       2.354372e+01                    1.906518e+01                   8.431577e+00                4.482283e+00                       8.570568e+00
LAS1L                                    2.439290e+01                       3.699727e+01                    2.130814e+01                   4.953552e+01                5.199448e+01                       3.915863e+01
ENPP4                                    1.478357e+00                       7.474196e+00                    0.000000e+00                   3.513157e+00                8.964565e-01                       6.649579e+00
SEMA3F                                   3.474140e+01                       3.276189e+01                    5.495257e+01                   3.161842e+01                1.972204e+01                       2.659831e+01
ANKIB1                                   9.609323e+00                       2.429114e+01                    4.485924e+00                   1.510658e+01                8.964565e+00                       2.541617e+01
                          X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6                                       5.266122e+00                   8.784613e+00                6.669063e+00                       1.124806e+01                    4.196805e+00                   8.759837e+00
TNMD                                         3.989486e-01                   1.421040e+00                0.000000e+00                       9.998279e-01                    0.000000e+00                   3.322697e+00
DPM1                                         1.196846e+01                   1.098077e+01                9.880093e+00                       1.291444e+01                    1.869486e+01                   1.258597e+01
SCYL3                                        2.074533e+00                   3.875565e-01                3.705035e+00                       2.249613e+00                    5.341389e+00                   3.322697e+00
C1orf112                                     4.787383e-01                   2.583710e-01                2.470023e-01                       6.665519e-01                    4.196805e+00                   8.055022e-01
FGR                                          5.928376e+01                   2.829162e+01                3.532133e+01                       1.399759e+01                    3.357444e+01                   2.094306e+01
CFH                                          3.111799e+00                   2.066968e+00                2.964028e+00                       2.166294e+00                    6.867500e+00                   3.826136e+00
FUCA2                                        1.643668e+01                   1.886108e+01                2.939328e+01                       1.624720e+01                    1.449805e+01                   1.550592e+01
GCLC                                         2.433587e+01                   4.211447e+01                1.926618e+01                       3.699363e+01                    2.518083e+01                   3.373041e+01
NFYA                                         2.816577e+01                   3.113370e+01                3.235730e+01                       3.241109e+01                    3.166680e+01                   3.473728e+01
STPG1                                        4.069276e+00                   5.813347e+00                9.880093e-01                       8.165261e+00                    5.722916e+00                   8.256398e+00
NIPAL3                                       1.260678e+01                   1.072240e+01                8.645081e+00                       9.665003e+00                    4.578333e+00                   1.037084e+01
LAS1L                                        3.430958e+01                   4.095180e+01                2.519424e+01                       3.649372e+01                    2.479930e+01                   4.218818e+01
ENPP4                                        4.867173e+00                   4.004750e+00                4.199040e+00                       5.998967e+00                    1.220889e+01                   3.020633e+00
SEMA3F                                       4.252792e+01                   1.847352e+01                5.063548e+01                       2.082975e+01                    4.502028e+01                   2.728639e+01
ANKIB1                                       1.715479e+01                   1.731086e+01                1.086810e+01                       2.557893e+01                    1.487958e+01                   1.611004e+01
                          X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6                                   3.298954e+00                       7.738225e+00                    1.891786e+01                   6.898157e+00                1.616451e+01                       9.547951e+00
TNMD                                     0.000000e+00                       9.401581e-01                    0.000000e+00                   0.000000e+00                0.000000e+00                       0.000000e+00
DPM1                                     9.996831e+00                       1.923708e+01                    7.882441e+00                   8.779472e+00                1.034529e+01                       1.291782e+01
SCYL3                                    3.998732e+00                       3.182074e+00                    9.458929e+00                   2.383000e+00                2.586322e+00                       1.067124e+01
C1orf112                                 5.998099e-01                       6.508787e-01                    0.000000e+00                   1.128789e+00                1.293161e+00                       0.000000e+00
FGR                                      4.498574e+01                       4.223480e+01                    8.118914e+01                   4.496344e+01                6.034751e+01                       2.527399e+01
CFH                                      5.298320e+00                       2.169596e+00                    7.882441e-01                   1.630473e+00                2.155268e-01                       1.123288e+00
FUCA2                                    1.009680e+01                       1.113726e+01                    2.837679e+01                   1.141331e+01                2.413900e+01                       1.572604e+01
GCLC                                     2.769122e+01                       2.596283e+01                    2.837679e+01                   2.752992e+01                1.810425e+01                       2.190412e+01
NFYA                                     2.619170e+01                       4.049912e+01                    2.128259e+01                   2.959936e+01                2.543217e+01                       1.291782e+01
STPG1                                    2.499208e+00                       4.700791e+00                    1.812961e+01                   4.389736e+00                7.758966e+00                       7.301375e+00
NIPAL3                                   1.099651e+01                       1.193278e+01                    1.497664e+01                   1.329463e+01                1.961294e+01                       5.616442e+00
LAS1L                                    3.568869e+01                       3.876344e+01                    3.704747e+01                   2.677739e+01                2.823401e+01                       2.639728e+01
ENPP4                                    1.899398e+00                       5.207030e+00                    0.000000e+00                   4.264315e+00                5.172644e+00                       3.369865e+00
SEMA3F                                   7.397655e+01                       3.362873e+01                    4.098869e+01                   3.373826e+01                4.116562e+01                       1.123288e+01
ANKIB1                                   1.199620e+01                       1.815228e+01                    1.734137e+01                   1.617931e+01                1.508688e+01                       5.054798e+00
                          X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6                                       1.482772e+00                   1.965155e+00                       2.321636e+01                    1.333434e+01                5.937025e+00                      1.341001e+00
TNMD                                         0.000000e+00                   0.000000e+00                       0.000000e+00                    0.000000e+00                0.000000e+00                      0.000000e+00
DPM1                                         1.235643e+01                   3.275259e+00                       1.428699e+01                    1.107776e+01                9.499241e+00                      8.381254e+00
SCYL3                                        1.977029e+00                   3.930311e+00                       4.911153e+00                    3.282300e+00                4.987101e+00                      0.000000e+00
C1orf112                                     0.000000e+00                   0.000000e+00                       4.464684e-01                    1.230863e+00                0.000000e+00                      0.000000e+00
FGR                                          6.672474e+01                   1.319929e+02                       2.366283e+01                    4.308019e+01                4.440895e+01                      9.923404e+01
CFH                                          9.390890e+00                   1.310104e+00                       4.464684e+00                    4.923450e+00                3.087253e+00                      2.346751e+00
FUCA2                                        4.942573e+00                   3.308012e+01                       1.294758e+01                    1.271891e+01                2.493551e+01                      1.139850e+01
GCLC                                         7.908118e+00                   2.030661e+01                       1.473346e+01                    1.682179e+01                1.852352e+01                      3.117826e+01
NFYA                                         1.532198e+01                   1.473867e+01                       2.053755e+01                    2.789955e+01                1.139909e+01                      3.453076e+01
STPG1                                        2.965544e+00                   6.550518e+00                       9.375837e+00                    5.128594e+00                8.311836e+00                      6.705003e-01
NIPAL3                                       3.064396e+01                   1.506619e+01                       1.651933e+01                    1.415492e+01                1.543627e+01                      1.575676e+01
LAS1L                                        2.767841e+01                   4.323342e+01                       3.125279e+01                    4.041332e+01                3.419727e+01                      4.559402e+01
ENPP4                                        5.436831e+00                   2.620207e+00                       2.232342e+00                    1.846294e+00                2.137329e+00                      7.710753e+00
SEMA3F                                       2.965544e+01                   2.652960e+01                       2.678811e+00                    4.082361e+01                4.013429e+01                      2.045026e+01
ANKIB1                                       1.037940e+01                   1.604877e+01                       2.768104e+01                    1.292406e+01                8.549317e+00                      1.676251e+01
                          X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                                      9.873680e+00               7.170684e+00
TNMD                                        0.000000e+00               0.000000e+00
DPM1                                        2.675449e+01               3.073150e+01
SCYL3                                       1.911035e+00               1.024383e+00
C1orf112                                    0.000000e+00               0.000000e+00
FGR                                         1.226247e+02               9.424327e+01
CFH                                         1.274023e+01               1.024383e+01
FUCA2                                       1.911035e+01               0.000000e+00
GCLC                                        1.337724e+01               1.434137e+01
NFYA                                        1.688081e+01               3.482903e+01
STPG1                                       0.000000e+00               9.219450e+00
NIPAL3                                      1.496977e+01               1.536575e+01
LAS1L                                       3.726518e+01               2.048767e+01
ENPP4                                       3.503564e+00               2.048767e+00
SEMA3F                                      3.981322e+01               2.356082e+01
ANKIB1                                      8.281151e+00               6.146300e+00
 [ reached getOption("max.print") -- omitted 25439 rows ]

$tibia_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
         (Intercept) patientX104 patientX105 patientX109 patientX128 patientX130 patientX144 patientX148 patientX149 patientX151 patientX155 patientX156 patientX159  patientX160 patientX161 patientX163 patientX164
TSPAN6     -12.25172  0.04406928  0.84019247  0.60588199  0.16165295   0.1244473  0.06794798 -0.02625455   0.7528399  1.07888329  0.22129102  1.01215762   0.4478837  0.358302596   0.9182398 -0.12645603   1.0748605
TNMD       -17.07707  1.59157950  4.95629013  2.32100432 -0.21219890  -0.2794509  3.49152043  1.82692534   3.1336725 -0.26591528 -0.18256384  2.66132364   3.5603833  4.140584975   2.1456256 -0.07524611  -0.1091402
DPM1       -11.15592  0.06873637 -0.62448403 -0.06318352 -0.09346094   0.2743371  0.11620614  0.33543622  -0.4111354  0.03501757 -0.09771562 -0.08282952  -0.1776007  0.006748076  -0.1329719 -0.39529075  -0.1662029
SCYL3      -11.98020 -0.03834093  0.04117712 -0.38786677 -0.68384443  -0.5999563 -0.34575741 -0.87746903  -0.5255504 -0.25832922 -1.75449122 -0.68998705  -0.7370011 -0.463595136  -0.3606641 -0.09923204  -0.3076573
C1orf112   -12.94608 -0.48959117 -4.04063893  0.71374233 -2.08926183  -0.6449300  0.32655119  0.12371514  -1.5649092 -1.52956438 -1.68616890 -0.69943085  -1.4028547 -0.052684280  -0.1845621 -4.17846401  -1.2934729
         patientX99 groupsclerotic
TSPAN6    0.2287480     0.04349959
TNMD     -0.2980981    -0.93351400
DPM1      0.4825022    -0.14390015
SCYL3    -1.8057150    -0.11344632
C1orf112 -4.4298734    -1.06861775
25450 more rows ...

$fitted.values
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6                      5.344491e+01                   1.489758e+01                1.522931e+01                         13.1146519                      15.6997911                       1.588054e+01
TNMD                        2.409608e-09                   1.508575e-10                1.542168e-10                          0.4309118                       0.5158525                       9.596770e+00
DPM1                        1.605415e+02                   3.707124e+01                3.789672e+01                         40.3520364                      48.3061652                       1.097138e+01
SCYL3                       7.028191e+01                   1.671522e+01                1.708743e+01                         15.8584516                      18.9844442                       9.357692e+00
C1orf112                    2.649991e+01                   2.212895e+00                2.262171e+00                          3.7937869                       4.5416121                       3.201364e-08
         X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6                     2.312673e+01                          38.234234                     40.5239878                  43.0749164                       1.264395e+01                    5.900477e+01
TNMD                       3.138956e+00                           1.655666                      0.3941339                   0.4189441                       3.773348e-10                    1.760886e-09
DPM1                       1.323581e+01                          58.658034                     51.5024375                  54.7444442                       2.938504e+01                    1.371294e+02
SCYL3                      1.162725e+01                          18.526529                     16.7537931                  17.8084210                       7.097339e+00                    3.312073e+01
C1orf112                   1.396661e-08                          23.082183                      7.3289843                   7.7903337                       6.070175e-01                    2.832733e+00
         X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6                     6.295189e+00                1.023057e+01                       1.934575e+01                    4.222221e+01                   5.690182e+00                3.960587e+00
TNMD                       4.219531e-11                6.857334e-11                       5.598321e-10                    1.221837e-09                   3.698364e-11                2.574204e-11
DPM1                       1.211973e+01                1.969627e+01                       6.749719e+01                    1.473130e+02                   1.644624e+01                1.144722e+01
SCYL3                      3.014956e+00                4.899729e+00                       1.226809e+01                    2.677517e+01                   3.078766e+00                2.142940e+00
C1orf112                   9.053873e-02                1.471382e-01                       4.435651e+00                    9.680835e+00                   3.908455e-01                2.720436e-01
         X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6                             70.89719                        50.11163                      45.123111                   18.198427                          28.253889                        92.09166
TNMD                               27.96827                        19.76857                       3.998038                    1.612433                           1.321478                         4.30727
DPM1                              223.39880                       157.90301                     117.785374                   47.503563                         121.970962                       397.55616
SCYL3                              61.48895                        43.46170                      33.390772                   13.466703                          15.764700                        51.38398
C1orf112                           48.08741                        33.98920                       9.168716                    3.697799                          16.426812                        53.54209
         X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6                       3.32685727                          47.513181                      19.2650826                     31.1332826                   7.9194927                       3.139009e+01
TNMD                         0.03494839                           4.223713                       1.7125812                      0.6216078                   0.1581208                       3.472172e-10
DPM1                        11.89742238                          44.383901                      17.9962591                     24.0922175                   6.1284299                       3.307912e+01
SCYL3                        1.58380220                          17.297378                       7.0135364                      9.6705329                   2.4599306                       1.078385e+01
C1orf112                     0.57945053                           2.281451                       0.9250559                      0.4478465                   0.1139204                       1.102016e+00
         X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6                      4.929200e+01                   8.409561e+00                9.467003e+00                       5.021394e+01                    2.145622e+01                   1.381350e+01
TNMD                        5.452367e-10                   2.089263e-11                2.351973e-11                       1.443593e-09                    6.168413e-10                   8.919395e-11
DPM1                        5.194429e+01                   7.341338e+00                8.264458e+00                       1.094567e+02                    4.677043e+01                   2.494379e+01
SCYL3                       1.693392e+01                   2.464982e+00                2.774936e+00                       8.967997e+00                    3.831989e+00                   2.104914e+00
C1orf112                    1.730500e+00                   8.844547e-02                9.956686e-02                       3.486952e+00                    1.489960e+00                   2.873641e-01
         X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6                  8.388777e+00                         105.289845                      11.6952038                     39.0120451                  15.2885771                          50.410794
TNMD                    5.416643e-11                           4.441261                       0.4933187                      0.3695982                   0.1448432                          12.884750
DPM1                    1.514807e+01                         105.396217                      11.7070192                     32.3502584                  12.6778645                          80.801015
SCYL3                   1.278289e+00                          25.031901                       2.7804503                      7.9134411                   3.1012282                          20.121823
C1orf112                1.745128e-01                           9.447006                       1.0493382                      1.0486089                   0.4109433                           3.840084
         X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6                         93.359429                      60.254296                  31.5137943                           81.72363                       17.847013                      70.666160
TNMD                           23.862209                       3.459009                   1.8091077                           45.24704                        9.881162                       8.787499
DPM1                          149.641299                      80.005860                  41.8441238                          172.37450                       37.643577                     123.474518
SCYL3                          37.265073                      20.520650                  10.7325717                           47.01946                       10.268229                      34.689721
C1orf112                        7.111732                       1.375031                   0.7191592                           27.75975                        6.062245                       7.190955
         X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6                     71.174743                         165.064544                       15.144349                     198.915006                   57.877079                       7.448451e+00
TNMD                        8.850742                           4.194117                        0.384802                       1.135182                    0.330297                       3.039280e-10
DPM1                      124.363162                         172.650299                       15.840327                     172.354087                   50.148811                       1.708884e+01
SCYL3                      34.939383                          60.056705                        5.510085                      61.749660                   17.966920                       1.006046e+01
C1orf112                    7.242708                          28.998964                        2.660598                      10.468956                    3.046088                       3.307160e-08
         X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6                      8.463970e+00                   1.334683e+01                       3.128566e+01                    6.808912e+01                6.146158e+01                      1.783278e+01
TNMD                        3.453654e-10                   1.223191e-10                       3.694867e-10                    8.041393e-10                1.630304e-10                      4.221172e-10
DPM1                        1.941872e+01                   2.536677e+01                       2.704933e+01                    5.886930e+01                4.402054e+01                      6.899054e+01
SCYL3                       1.143210e+01                   1.538116e+01                       1.026548e+01                    2.234147e+01                1.720668e+01                      2.994818e+00
C1orf112                    3.758057e-08                   1.775312e-08                       1.394713e+00                    3.035410e+00                8.208248e-01                      4.924430e-08
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                     1.877028e+01               6.098487e+00
TNMD                       4.443086e-10               3.242257e-11
DPM1                       7.261748e+01               1.954488e+01
SCYL3                      3.152260e+00               8.738418e-01
C1orf112                   5.183315e-08               5.045058e-09
25450 more rows ...

$deviance
[1] 64.18447 22.23679 26.23842 32.44059 29.32841
25450 more elements ...

$iter
[1]  8 22  6  7 18
25450 more elements ...

$failed
[1] FALSE FALSE FALSE FALSE FALSE
25450 more elements ...

$method
[1] "levenberg"

$counts
         X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6                                 3                             18                          28                                 12                              17                                 26
TNMD                                   0                              0                           0                                  0                               1                                 10
DPM1                                 177                             29                          42                                 33                              57                                  6
SCYL3                                 61                             26                          10                                 26                               7                                 14
C1orf112                              71                              0                           0                                  0                               9                                  0
         X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6                                9                                 43                             45                          33                                 16                              75
TNMD                                  3                                  4                              0                           0                                  0                               0
DPM1                                 19                                 70                             62                          33                                 34                             153
SCYL3                                 6                                 10                             13                          30                                  4                              24
C1orf112                              0                                  1                             22                           0                                  0                               6
         X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6                                5                           6                                 28                               4                              3                           9
TNMD                                  0                           0                                  0                               0                              0                           0
DPM1                                  6                          23                                 38                             159                             13                          19
SCYL3                                 5                           6                                  8                              16                              0                           7
C1orf112                              0                           0                                  2                              23                              0                           0
         X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6                                   65                              26                             62                          22                                 33                              17
TNMD                                      1                               0                              0                           7                                  3                               0
DPM1                                    174                             218                            105                          45                                101                             356
SCYL3                                    50                              38                             31                          19                                 18                              37
C1orf112                                 16                              37                             14                           4                                 19                              75
         X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6                                7                                 59                              15                             33                           7                                  4
TNMD                                  0                                 13                               0                              0                           0                                  0
DPM1                                 16                                 66                              20                             27                           0                                 26
SCYL3                                 2                                 12                               4                             21                           1                                 11
C1orf112                              0                                  0                               0                              2                           0                                  0
         X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6                                42                              0                          30                                 43                              29                             16
TNMD                                   0                              0                           0                                  0                               0                              0
DPM1                                  48                             15                           3                                 96                              45                             28
SCYL3                                 23                              0                           4                                 21                               0                              1
C1orf112                               4                              0                           0                                  3                               3                              0
         X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6                             5                                 75                              26                              7                          16                                 66
TNMD                               0                                 12                               0                              0                           0                                  8
DPM1                              16                                 59                              12                             26                          22                                 79
SCYL3                              1                                 38                               4                              5                           1                                 36
C1orf112                           0                                 10                               1                              0                           1                                  2
         X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6                                66                             68                          27                                135                              11                             87
TNMD                                   5                             11                           0                                 12                               0                             33
DPM1                                 150                             85                          40                                155                              49                            125
SCYL3                                 26                              3                          15                                 27                              14                             33
C1orf112                               6                              2                           1                                  8                              11                              8
         X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6                            33                                107                              24                            110                          75                                 17
TNMD                               0                                 13                               0                              0                           0                                  0
DPM1                             100                                266                              10                            140                          48                                 23
SCYL3                             40                                 44                              12                             38                          12                                 19
C1orf112                           6                                  9                               0                             18                           6                                  0
         X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6                                 3                              6                                 52                              65                          25                                 4
TNMD                                   0                              0                                  0                               0                           0                                 0
DPM1                                  25                             10                                 32                              54                          40                                25
SCYL3                                  4                             12                                 11                              16                          21                                 0
C1orf112                               0                              0                                  1                               6                           0                                 0
         X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6                               31                          7
TNMD                                  0                          0
DPM1                                 84                         30
SCYL3                                 6                          1
C1orf112                              0                          0
25450 more rows ...

$unshrunk.coefficients
         (Intercept) patientX104  patientX105 patientX109 patientX128 patientX130 patientX144 patientX148 patientX149 patientX151 patientX155 patientX156 patientX159  patientX160 patientX161 patientX163 patientX164
TSPAN6     -12.25755  0.04478320   0.84363162  0.60858193  0.16293812   0.1250750  0.06856748 -0.02670748   0.7560022  1.08254262  0.22274700  1.01586840   0.4501357  0.360303891   0.9217194  -0.1268412   1.0788126
TNMD       -36.08000 20.45165457  24.16241695 21.29150717 -0.24967565  -0.3183288 22.96086067 20.73326559  22.1581629 -0.32256717 -0.22722357 21.67254299  22.9084281 23.591551124  21.0715188  -0.2266244  -0.2608003
DPM1       -11.15765  0.06879415  -0.62607410 -0.06332566 -0.09365573   0.2747873  0.11639440  0.33594356  -0.4120290  0.03505174 -0.09791717 -0.08302267  -0.1779809  0.006729252  -0.1332498  -0.3963228  -0.1665859
SCYL3      -11.98369 -0.03910725   0.04087282 -0.38980864 -0.68838362  -0.6042595 -0.34766866 -0.88402832  -0.5283130 -0.25976330 -1.77374632 -0.69456049  -0.7421276 -0.466340660  -0.3631909  -0.1000977  -0.3094233
C1orf112   -12.95906 -0.49407197 -18.47705653  0.80542184 -2.17192809  -0.6462131  0.38186723  0.13248649  -1.5786830 -1.56529866 -1.74300768 -0.69364055  -1.4230651 -0.017941884  -0.1158468 -18.6579279  -1.3301482
          patientX99 groupsclerotic
TSPAN6     0.2301995     0.04397152
TNMD      -0.4141237    -1.44945922
DPM1       0.4832296    -0.14428669
SCYL3     -1.8278183    -0.11477028
C1orf112 -18.7758008    -1.16141534
25450 more rows ...

$df.residual
[1] 43 43 43 43 43
25450 more elements ...

$design
                                   (Intercept) patientX104 patientX105 patientX109 patientX128 patientX130 patientX144 patientX148 patientX149 patientX151 patientX155 patientX156 patientX159 patientX160 patientX161
X102_tibia_non.sclerotic_pellet              1           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X102_tibia_sclerotic_adipocyte               1           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X102_tibia_sclerotic_pellet                  1           0           0           0           0           0           0           0           0           0           0           0           0           0           0
X104_tibia_non.sclerotic_adipocyte           1           1           0           0           0           0           0           0           0           0           0           0           0           0           0
X104_tibia_non.sclerotic_pellet              1           1           0           0           0           0           0           0           0           0           0           0           0           0           0
                                   patientX163 patientX164 patientX99 groupsclerotic
X102_tibia_non.sclerotic_pellet              0           0          0              0
X102_tibia_sclerotic_adipocyte               0           0          0              1
X102_tibia_sclerotic_pellet                  0           0          0              1
X104_tibia_non.sclerotic_adipocyte           0           0          0              0
X104_tibia_non.sclerotic_pellet              0           0          0              0
57 more rows ...

$offset
        [,1]     [,2]    [,3]    [,4]     [,5]     [,6]     [,7]    [,8]     [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]    [,17]   [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 16.2362 14.91478 14.9368 14.7865 14.96641 14.17901 14.51094 15.2927 15.30689 15.36794 14.63179 16.17223 13.89043 14.37602 15.09495 15.87542 13.82725 13.4649 16.45021 16.10324 15.95441 15.04635 15.62549 16.80704
        [,25]    [,26]    [,27]    [,28]   [,29]   [,30]    [,31]    [,32]    [,33]   [,34]    [,35]    [,36]    [,37]   [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]
[1,] 13.44231 15.36255 14.45984 14.89585 13.5269 14.6215 15.07277 13.26041 13.37885 15.9511 15.10082 14.61648 14.11773 15.8984 13.70086 14.86158 13.92482 15.72762 16.34387 15.86202 15.21387 16.30059 14.77908 16.11124
        [,49]    [,50]    [,51]    [,52]    [,53]   [,54]    [,55]   [,56]   [,57]    [,58]    [,59]    [,60]    [,61]    [,62]
[1,] 16.11841 16.44217 14.05346 16.58474 15.35018 14.3924 14.52021 14.9317 14.6219 15.39955 15.25318 14.90839 14.95963 13.79142
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1]  5 62
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
25450 more rows ...

$dispersion
[1] 0.4141750 3.8966115 0.3095450 0.7440241 2.1049333
25450 more elements ...

$prior.count
[1] 0.125

$AveLogCPM
[1]  3.1056355 -0.2543233  3.7623396  2.0162150  0.4687608
25450 more elements ...

$df.residual.zeros
[1] 43 23 43 43 38
25450 more elements ...

$df.prior
[1] 25.67789 25.67789 25.67789 25.67789 25.67789
25450 more elements ...

$var.post
[1] 1.3267538 0.8990513 0.7296690 0.9086660 0.8755580
25450 more elements ...

$var.prior
[1] 1.0489252 0.8383528 0.9297378 1.1669445 1.0291059
25450 more elements ...

$samples
57 more rows ...

$genes
25450 more rows ...


$tibia_sclerotic_vs_non_sclerotic$mds_plot
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.633991

$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.7924232

$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.503014

$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 2.270144


$tibia_sclerotic_vs_non_sclerotic$mds_plot$text
$tibia_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.842382 2.842382

$tibia_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 2.006003 1.741862



$tibia_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL

$tibia_sclerotic_vs_non_sclerotic$boxplot_gg


$volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic

$volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic

$volcano_hip_adipocytes_sclerotic_vs_non_sclerotic

$volcano_hip_pellet_sclerotic_vs_non_sclerotic

$volcano_hip_sclerotic_vs_non_sclerotic

$volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic

$volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic

$volcano_tibia_pellet_sclerotic_vs_non_sclerotic

$volcano_tibia_sclerotic_vs_non_sclerotic

volcano

plot_volcano <- function(results_table, 
                         gene_column = "genes", 
                         logFC_column = "logFC", 
                         FDR_column = "FDR", 
                         genes_of_interest = NULL, 
                         #output_file = paste0("volcano_plot.",format_plot),
                         output_file = NULL,
                         format_plot = "tiff",
                         up_color = "#d00000", 
                         down_color = "#3f88c5", 
                         ns_color = "#f2e9e4", 
                         up_size = 2, 
                         down_size = 2, 
                         ns_size = 1,
                         up_alpha = 1, 
                         down_alpha = 1, 
                         ns_alpha = 0.5,
                         x_limits = c(-10, 10),
                         y_threshold = -log10(0.05),
                         x_label = "Log2 Fold Change",
                         y_label = "-Log10 Adjusted P-Value") {
  
  # Mutate the gene type
  results_table <- results_table |>
    dplyr::mutate(gene_type = dplyr::case_when(
      !!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
      !!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
      TRUE ~ "Not selected"
    )) |>
    dplyr::filter(!!rlang::sym(gene_column) != "")
  
  # Get the top up and down genes
  ints_up <- results_table |>
    dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) > 1) |>
    dplyr::arrange(!!rlang::sym(FDR_column)) |>
    dplyr::slice(1:10) |>
    dplyr::pull(!!rlang::sym(gene_column))
  
  ints_down <- results_table |>
    dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) < -1) |>
    dplyr::arrange(!!rlang::sym(FDR_column)) |>
    dplyr::slice(1:10) |>
    dplyr::pull(!!rlang::sym(gene_column))
  
  ints <- c(ints_up, ints_down)
  
  ints_genes <- results_table |>
    dplyr::filter(!!rlang::sym(gene_column) %in% ints) |>
    dplyr::distinct(!!rlang::sym(gene_column), .keep_all = TRUE)
  
  if (!is.null(genes_of_interest)) {
    to_add_genes <- results_table |>
      dplyr::filter(!!rlang::sym(gene_column) %in% genes_of_interest) |> 
      dplyr::mutate(gene_type = dplyr::case_when(
        !!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
        !!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
        TRUE ~ "Not Selected"))
    results_table <- rbind(results_table, to_add_genes)
    ints_genes <- rbind(ints_genes, to_add_genes)
  }
  
  # Define the plot
  p <- results_table |>
    ggplot(aes(x = !!rlang::sym(logFC_column),
               y = -log10(!!rlang::sym(FDR_column)))) +
    geom_point(aes(colour = gene_type), 
               alpha = 0.8, 
               shape = 16,
               size = 1) +
    geom_hline(yintercept = y_threshold,
               linetype = "dashed") + 
    geom_vline(xintercept = c(log2(0.5), log2(2)),
               linetype = "dashed") +
    geom_point(data = dplyr::filter(ints_genes, gene_type == "up"),
               shape = 21,
               size = 2,
               fill = "tomato3", 
               colour = "black") + 
    geom_point(data = dplyr::filter(ints_genes, gene_type == "down"),
               shape = 21,
               size = 2,
               fill = "steelblue", 
               colour = "black") +
    geom_label_repel(data = ints_genes, # Add labels last to appear as the top layer  
                     aes(label = !!rlang::sym(gene_column)),
                     force = 2,
                     nudge_y = .2, nudge_x = 0.1,
                     max.overlaps = 30, size = 2) +
    scale_color_manual(values = c("Upregulated" = up_color,
                                  "Downregulated" = down_color,
                                  "Not Selected" = ns_color)) +
    scale_x_continuous(breaks = c(seq(-10, 10, 2)),     
                       limits = x_limits) +
    labs(x = x_label, y = y_label, color = "Genes") +#title = title

    #theme_void() +  # Remove background
    #theme(legend.position = "none")  # Remove legend if not needed
    theme_classic(base_size = 14) +
    theme(
    plot.title = element_text(hjust = 0.5, face = "bold"),
    legend.position = "right",
    legend.title = element_text(size = 12),
    legend.text = element_text(size = 10)
  )
  
  if (!is.null(genes_of_interest)) {
    p <- p + geom_point(data = to_add_genes,
                        shape = 21,
                        size = 2.4,
                        fill = "#70e000", 
                        colour = "black")
    }
  # Save the plot
  if (!is.null(output_file)) {
    ggsave(plot = p,
           filename = output_file,
           device = format_plot,
           dpi = 300,
           units = "in",
           width = 7, height = 12)
  }
  
  return(p)
}

HERE IF WANNA SAVE THE PLOT CHANGE THE OUTPUT FILE

#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[1]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic

#pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
comparison_names[8]
[1] "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[8]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic

Hips

comparison_names[5]
[1] "hip_adipocytes_sclerotic_vs_non_sclerotic"
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[5]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic

comparison_names[6]
[1] "hip_pellet_sclerotic_vs_non_sclerotic"
volcano_hip_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[6]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_pellet_sclerotic_vs_non_sclerotic

comparison_names[7]
[1] "hip_sclerotic_vs_non_sclerotic"
volcano_hip_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[7]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_sclerotic_vs_non_sclerotic

Tibias

comparison_names[9]
[1] "tibia_adipocytes_sclerotic_vs_non_sclerotic"
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[9]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic

comparison_names[10]
[1] "tibia_pellet_sclerotic_vs_non_sclerotic"
volcano_tibia_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[10]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_pellet_sclerotic_vs_non_sclerotic

comparison_names[11]
[1] "tibia_sclerotic_vs_non_sclerotic"
volcano_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[11]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_sclerotic_vs_non_sclerotic

comparison_names
 [1] "adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"         "bone_hip_vs_tibia"                                          "bone_non_sclerotic_hip_vs_tibia"                           
 [4] "bone_sclerotic_hip_vs_tibia"                                "hip_adipocytes_sclerotic_vs_non_sclerotic"                  "hip_pellet_sclerotic_vs_non_sclerotic"                     
 [7] "hip_sclerotic_vs_non_sclerotic"                             "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"           "tibia_adipocytes_sclerotic_vs_non_sclerotic"               
[10] "tibia_pellet_sclerotic_vs_non_sclerotic"                    "tibia_sclerotic_vs_non_sclerotic"                           "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"
[13] "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic" "volcano_hip_adipocytes_sclerotic_vs_non_sclerotic"          "volcano_hip_pellet_sclerotic_vs_non_sclerotic"             
[16] "volcano_hip_sclerotic_vs_non_sclerotic"                     "volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"   "volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic"       
[19] "volcano_tibia_pellet_sclerotic_vs_non_sclerotic"            "volcano_tibia_sclerotic_vs_non_sclerotic"                  
---
title: "Volcanos"
output: html_notebook
---

Before running this script, you need to run all the analysis first so the variable are available.

# run volcanos for all the comparisons of interest
```{r}

```


# Get comparisons 
```{r}
ls(all.names = TRUE)
# Get all object names that match a pattern
comparison_names <- ls(pattern = "vs")
comparison_names
```


```{r}
comparisons_list <- mget(comparison_names)
comparisons_list

```


# volcano
```{r}
plot_volcano <- function(results_table, 
                         gene_column = "genes", 
                         logFC_column = "logFC", 
                         FDR_column = "FDR", 
                         genes_of_interest = NULL, 
                         #output_file = paste0("volcano_plot.",format_plot),
                         output_file = NULL,
                         format_plot = "tiff",
                         up_color = "#d00000", 
                         down_color = "#3f88c5", 
                         ns_color = "#f2e9e4", 
                         up_size = 2, 
                         down_size = 2, 
                         ns_size = 1,
                         up_alpha = 1, 
                         down_alpha = 1, 
                         ns_alpha = 0.5,
                         x_limits = c(-10, 10),
                         y_threshold = -log10(0.05),
                         x_label = "Log2 Fold Change",
                         y_label = "-Log10 Adjusted P-Value") {
  
  # Mutate the gene type
  results_table <- results_table |>
    dplyr::mutate(gene_type = dplyr::case_when(
      !!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
      !!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
      TRUE ~ "Not selected"
    )) |>
    dplyr::filter(!!rlang::sym(gene_column) != "")
  
  # Get the top up and down genes
  ints_up <- results_table |>
    dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) > 1) |>
    dplyr::arrange(!!rlang::sym(FDR_column)) |>
    dplyr::slice(1:10) |>
    dplyr::pull(!!rlang::sym(gene_column))
  
  ints_down <- results_table |>
    dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) < -1) |>
    dplyr::arrange(!!rlang::sym(FDR_column)) |>
    dplyr::slice(1:10) |>
    dplyr::pull(!!rlang::sym(gene_column))
  
  ints <- c(ints_up, ints_down)
  
  ints_genes <- results_table |>
    dplyr::filter(!!rlang::sym(gene_column) %in% ints) |>
    dplyr::distinct(!!rlang::sym(gene_column), .keep_all = TRUE)
  
  if (!is.null(genes_of_interest)) {
    to_add_genes <- results_table |>
      dplyr::filter(!!rlang::sym(gene_column) %in% genes_of_interest) |> 
      dplyr::mutate(gene_type = dplyr::case_when(
        !!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
        !!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
        TRUE ~ "Not Selected"))
    results_table <- rbind(results_table, to_add_genes)
    ints_genes <- rbind(ints_genes, to_add_genes)
  }
  
  # Define the plot
  p <- results_table |>
    ggplot(aes(x = !!rlang::sym(logFC_column),
               y = -log10(!!rlang::sym(FDR_column)))) +
    geom_point(aes(colour = gene_type), 
               alpha = 0.8, 
               shape = 16,
               size = 1) +
    geom_hline(yintercept = y_threshold,
               linetype = "dashed") + 
    geom_vline(xintercept = c(log2(0.5), log2(2)),
               linetype = "dashed") +
    geom_point(data = dplyr::filter(ints_genes, gene_type == "up"),
               shape = 21,
               size = 2,
               fill = "tomato3", 
               colour = "black") + 
    geom_point(data = dplyr::filter(ints_genes, gene_type == "down"),
               shape = 21,
               size = 2,
               fill = "steelblue", 
               colour = "black") +
    geom_label_repel(data = ints_genes, # Add labels last to appear as the top layer  
                     aes(label = !!rlang::sym(gene_column)),
                     force = 2,
                     nudge_y = .2, nudge_x = 0.1,
                     max.overlaps = 30, size = 2) +
    scale_color_manual(values = c("Upregulated" = up_color,
                                  "Downregulated" = down_color,
                                  "Not Selected" = ns_color)) +
    scale_x_continuous(breaks = c(seq(-10, 10, 2)),     
                       limits = x_limits) +
    labs(x = x_label, y = y_label, color = "Genes") +#title = title

    #theme_void() +  # Remove background
    #theme(legend.position = "none")  # Remove legend if not needed
    theme_classic(base_size = 14) +
    theme(
    plot.title = element_text(hjust = 0.5, face = "bold"),
    legend.position = "right",
    legend.title = element_text(size = 12),
    legend.text = element_text(size = 10)
  )
  
  if (!is.null(genes_of_interest)) {
    p <- p + geom_point(data = to_add_genes,
                        shape = 21,
                        size = 2.4,
                        fill = "#70e000", 
                        colour = "black")
    }
  # Save the plot
  if (!is.null(output_file)) {
    ggsave(plot = p,
           filename = output_file,
           device = format_plot,
           dpi = 300,
           units = "in",
           width = 7, height = 12)
  }
  
  return(p)
}

```


## HERE IF WANNA SAVE THE PLOT CHANGE THE OUTPUT FILE

```{r}
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[1]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic

```

```{r}
#pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
comparison_names[8]
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[8]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
```

# Hips
```{r}
comparison_names[5]
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[5]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic
```
```{r}
comparison_names[6]
volcano_hip_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[6]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_pellet_sclerotic_vs_non_sclerotic
```


```{r}
comparison_names[7]
volcano_hip_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[7]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_sclerotic_vs_non_sclerotic
```
# Tibias
```{r}
comparison_names[9]
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[9]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic
```
```{r}
comparison_names[10]
volcano_tibia_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[10]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_pellet_sclerotic_vs_non_sclerotic
```
```{r}
comparison_names[11]
volcano_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[11]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_sclerotic_vs_non_sclerotic
```

```{r}
comparison_names
```

